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>
graeter-group · Mar 7, 2024 · 8f3fbc7 · 8f3fbc7
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diff --git 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
@@ -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
@@ -537,39 +537,39 @@ <h1 class="title">How-To</h1>
 </tr>
 </thead>
 <tbody class="list">
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+<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>
 <td>
 <span class="listing-author">&nbsp;</span>
 </td>
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-<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>
 <td>
 <span class="listing-author">&nbsp;</span>
 </td>
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-<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>
 <td>
 <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>
 <td>
 <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
@@ -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
@@ -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>
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 </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">
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-<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
@@ -2,154 +2,154 @@
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-    <lastmod>2024-03-06T15:45:45.017Z</lastmod>
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-    <lastmod>2024-03-06T15:45:45.021Z</lastmod>
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     <loc>http://hits-mbm-dev.github.io/kimmdy/guide/references/input.html</loc>
-    <lastmod>2024-03-06T15:45:45.013Z</lastmod>
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diff --git 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