From 8f3fbc715ff8298df46bf40e7a9a6a7e32aa13d1 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 7 Mar 2024 09:09:21 +0100
Subject: [PATCH] chore(main): release 6.3.0 (#397)

* chore(main): release 6.3.0

* chore(docs): render docs

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
---
 CHANGELOG.md                              | 13 ++++
 docs/guide/explanation/index.html         |  2 +-
 docs/guide/how-to/index.html              | 10 +--
 docs/guide/tutorials/getting-started.html |  2 +-
 docs/guide/tutorials/index.html           |  6 +-
 docs/sitemap.xml                          | 76 +++++++++++------------
 setup.cfg                                 |  2 +-
 7 files changed, 62 insertions(+), 49 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fbc09ce7..3a7a5307 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,18 @@
 # Changelog
 
+## [6.3.0](https://github.com/hits-mbm-dev/kimmdy/compare/v6.2.5...v6.3.0) (2024-03-07)
+
+
+### Features
+
+* allow customizing trjconv output group ([#396](https://github.com/hits-mbm-dev/kimmdy/issues/396)) ([97b5588](https://github.com/hits-mbm-dev/kimmdy/commit/97b55880a791436c22d8c474d2d88541051f831b))
+* analysis radical migration tool ([#388](https://github.com/hits-mbm-dev/kimmdy/issues/388)) ([ba4cb0f](https://github.com/hits-mbm-dev/kimmdy/commit/ba4cb0f12224c6801e21a2961a52e3f3c3172fc1))
+
+
+### Bug Fixes
+
+* squiggly lines begone ([#399](https://github.com/hits-mbm-dev/kimmdy/issues/399)) ([b1210e4](https://github.com/hits-mbm-dev/kimmdy/commit/b1210e44f222204a67e1385ce8467ff7e41dabd2))
+
 ## [6.2.5](https://github.com/hits-mbm-dev/kimmdy/compare/v6.2.4...v6.2.5) (2024-02-27)
 
 
diff --git a/docs/guide/explanation/index.html b/docs/guide/explanation/index.html
index bd292ffc..9b53f88a 100644
--- a/docs/guide/explanation/index.html
+++ b/docs/guide/explanation/index.html
@@ -537,7 +537,7 @@ <h1 class="title">Explanations</h1>
 </tr>
 </thead>
 <tbody class="list">
-<tr data-index="0" data-listing-file-modified-sort="1709739945013" 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="1709798634957" data-listing-reading-time-sort="1" 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>
diff --git a/docs/guide/how-to/index.html b/docs/guide/how-to/index.html
index 0696cb1d..a785bea3 100644
--- a/docs/guide/how-to/index.html
+++ b/docs/guide/how-to/index.html
@@ -537,7 +537,7 @@ <h1 class="title">How-To</h1>
 </tr>
 </thead>
 <tbody class="list">
-<tr data-index="0" data-listing-file-modified-sort="1709739945013" 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="1709798634957" data-listing-reading-time-sort="2" data-listing-title-sort="Contribute" data-listing-filename-sort="contribute.qmd">
 <td>
 <a href="../../guide/how-to/contribute.html" class="title listing-title">Contribute</a>
 </td>
@@ -545,7 +545,7 @@ <h1 class="title">How-To</h1>
 <span class="listing-author">&nbsp;</span>
 </td>
 </tr>
-<tr data-index="1" data-listing-file-modified-sort="1709739945013" data-listing-reading-time-sort="1" data-listing-title-sort="Examples" data-listing-filename-sort="examples.qmd">
+<tr data-index="1" data-listing-file-modified-sort="1709798634957" data-listing-reading-time-sort="1" data-listing-title-sort="Examples" data-listing-filename-sort="examples.qmd">
 <td>
 <a href="../../guide/how-to/examples.html" class="title listing-title">Examples</a>
 </td>
@@ -553,7 +553,7 @@ <h1 class="title">How-To</h1>
 <span class="listing-author">&nbsp;</span>
 </td>
 </tr>
-<tr data-index="2" data-listing-file-modified-sort="1709739945013" data-listing-reading-time-sort="1" data-listing-title-sort="High Performance Computing" data-listing-filename-sort="hcp.qmd">
+<tr data-index="2" data-listing-file-modified-sort="1709798634957" data-listing-reading-time-sort="1" data-listing-title-sort="High Performance Computing" data-listing-filename-sort="hcp.qmd">
 <td>
 <a href="../../guide/how-to/hcp.html" class="title listing-title">High Performance Computing</a>
 </td>
@@ -561,7 +561,7 @@ <h1 class="title">How-To</h1>
 <span class="listing-author">&nbsp;</span>
 </td>
 </tr>
-<tr data-index="3" data-listing-file-modified-sort="1709739945013" data-listing-reading-time-sort="1" data-listing-title-sort="Install Machine Learning Plugins" data-listing-filename-sort="install-ml-plugins.qmd">
+<tr data-index="3" data-listing-file-modified-sort="1709798634957" data-listing-reading-time-sort="1" 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 +569,7 @@ <h1 class="title">How-To</h1>
 <span class="listing-author">&nbsp;</span>
 </td>
 </tr>
-<tr data-index="4" data-listing-file-modified-sort="1709739945013" data-listing-reading-time-sort="1" data-listing-title-sort="Reaction only" data-listing-filename-sort="reaction_only.qmd">
+<tr data-index="4" data-listing-file-modified-sort="1709798634957" data-listing-reading-time-sort="1" 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>
 </td>
diff --git a/docs/guide/tutorials/getting-started.html b/docs/guide/tutorials/getting-started.html
index 90decd3d..280c7330 100644
--- a/docs/guide/tutorials/getting-started.html
+++ b/docs/guide/tutorials/getting-started.html
@@ -603,7 +603,7 @@ <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", {"layoutShowLeftPanel":true,"layoutIsExpanded":false,"viewportShowAnimation":true,"layoutShowRemoteState":false,"layoutShowLog":false,"viewportShowExpand":true,"viewportShowSelectionMode":false,"emdbProvider":"rcsb","layoutShowControls":false,"layoutShowSequence":false,"pdbProvider":"rcsb"}).then(viewer => {
+    molstar.Viewer.create("app-./getting-started-files/vis-ala.molj", {"layoutIsExpanded":false,"viewportShowAnimation":true,"emdbProvider":"rcsb","viewportShowSelectionMode":false,"viewportShowExpand":true,"layoutShowRemoteState":false,"layoutShowSequence":false,"layoutShowLog":false,"pdbProvider":"rcsb","layoutShowLeftPanel":true,"layoutShowControls":false}).then(viewer => {
     viewer.loadSnapshotFromUrl(url="./getting-started-files/vis-ala.molj", "molj");    });
     </script>
     
diff --git a/docs/guide/tutorials/index.html b/docs/guide/tutorials/index.html
index a5b905ec..120af758 100644
--- a/docs/guide/tutorials/index.html
+++ b/docs/guide/tutorials/index.html
@@ -507,7 +507,7 @@ <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="1709739945017" data-listing-reading-time-sort="3">
+<div class="quarto-post image-right" data-index="0" data-categories="user" data-listing-file-modified-sort="1709798634957" data-listing-reading-time-sort="3">
 <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>
 </div>
@@ -539,7 +539,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="1" data-categories="user" data-listing-file-modified-sort="1709739945013" data-listing-reading-time-sort="6">
+<div class="quarto-post image-right" data-index="1" data-categories="user" data-listing-file-modified-sort="1709798634957" data-listing-reading-time-sort="6">
 <div class="thumbnail">
 <p><a href="../../guide/tutorials/colbuilder.html"> <img src="../../guide/tutorials/img/colbuilder.png" class="thumbnail-image"> </a></p>
 </div>
@@ -571,7 +571,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="2" data-categories="developer" data-listing-file-modified-sort="1709739945021" data-listing-reading-time-sort="6">
+<div class="quarto-post image-right" data-index="2" data-categories="developer" data-listing-file-modified-sort="1709798634961" data-listing-reading-time-sort="6">
 <div class="thumbnail">
 <p><a href="../../guide/tutorials/write-plugin.html"> <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div> </a></p>
 </div>
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 31b3ed49..1f3b1893 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -2,154 +2,154 @@
 <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>2024-03-06T15:45:45.013Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.957Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/getting-started.html</loc>
-    <lastmod>2024-03-06T15:45:45.017Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.957Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/write-plugin.html</loc>
-    <lastmod>2024-03-06T15:45:45.021Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.961Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/references/input.html</loc>
-    <lastmod>2024-03-06T15:45:45.013Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.957Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/install-ml-plugins.html</loc>
-    <lastmod>2024-03-06T15:45:45.013Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.957Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/hcp.html</loc>
-    <lastmod>2024-03-06T15:45:45.013Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.957Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/contribute.html</loc>
-    <lastmod>2024-03-06T15:45:45.013Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.957Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/utils.html</loc>
-    <lastmod>2024-03-06T15:47:26.625Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.389Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/index.html</loc>
-    <lastmod>2024-03-06T15:47:26.209Z</lastmod>
+    <lastmod>2024-03-07T08:05:19.977Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.ff.html</loc>
-    <lastmod>2024-03-06T15:47:26.265Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.033Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/parsing.html</loc>
-    <lastmod>2024-03-06T15:47:26.477Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.245Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.topology.html</loc>
-    <lastmod>2024-03-06T15:47:26.261Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.029Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/homolysis.reaction.Homolysis.html</loc>
-    <lastmod>2024-03-06T15:47:26.625Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.393Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/dummyreaction.reaction.DummyReaction.html</loc>
-    <lastmod>2024-03-06T15:47:26.629Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.397Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/coordinates.html</loc>
-    <lastmod>2024-03-06T15:47:26.429Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.197Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/runmanager.html</loc>
-    <lastmod>2024-03-06T15:47:26.545Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.309Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/plugins.html</loc>
-    <lastmod>2024-03-06T15:47:26.489Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.253Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/tools.html</loc>
-    <lastmod>2024-03-06T15:47:26.597Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.361Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/schema.html</loc>
-    <lastmod>2024-03-06T15:47:26.561Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.325Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/index.html</loc>
-    <lastmod>2024-03-06T15:45:45.021Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.961Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/analysis.html</loc>
-    <lastmod>2024-03-06T15:47:26.385Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.153Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/config.html</loc>
-    <lastmod>2024-03-06T15:47:26.405Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.173Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/parsing.TopologyDict.html</loc>
-    <lastmod>2024-03-06T15:47:26.353Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.117Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/constants.html</loc>
-    <lastmod>2024-03-06T15:47:26.409Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.177Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.atomic.html</loc>
-    <lastmod>2024-03-06T15:47:26.349Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.117Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/recipe.html</loc>
-    <lastmod>2024-03-06T15:47:26.533Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.297Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/topology.utils.html</loc>
-    <lastmod>2024-03-06T15:47:26.289Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.057Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/hat_naive.reaction.NaiveHAT.html</loc>
-    <lastmod>2024-03-06T15:47:26.629Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.393Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/kmc.html</loc>
-    <lastmod>2024-03-06T15:47:26.449Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.217Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/cmd.html</loc>
-    <lastmod>2024-03-06T15:47:26.233Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.001Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/_reference/tasks.html</loc>
-    <lastmod>2024-03-06T15:47:26.573Z</lastmod>
+    <lastmod>2024-03-07T08:05:20.341Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/reaction_only.html</loc>
-    <lastmod>2024-03-06T15:45:45.013Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.957Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/examples.html</loc>
-    <lastmod>2024-03-06T15:45:45.013Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.957Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/how-to/index.html</loc>
-    <lastmod>2024-03-06T15:45:45.013Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.957Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/references/cmd_ref.html</loc>
-    <lastmod>2024-03-06T15:45:45.013Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.957Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/colbuilder.html</loc>
-    <lastmod>2024-03-06T15:45:45.013Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.957Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/tutorials/index.html</loc>
-    <lastmod>2024-03-06T15:45:45.021Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.961Z</lastmod>
   </url>
   <url>
     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/explanation/topology.html</loc>
-    <lastmod>2024-03-06T15:45:45.013Z</lastmod>
+    <lastmod>2024-03-07T08:03:54.957Z</lastmod>
   </url>
 </urlset>
diff --git a/setup.cfg b/setup.cfg
index da2fa1c9..3ce7dfe8 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = kimmdy
-version = 6.2.5
+version = 6.3.0
 license = MIT
 description = Kinetic Monte Carlo Molecular Dynamics
 description_content_type = text/markdown