chore(main): release 6.6.0 (#423)

* chore(main): release 6.6.0

* 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>

Author: github-actions[bot]

CHANGELOG.md

@@ -1,5 +1,25 @@
 # Changelog
 
+## [6.6.0](https://github.com/hits-mbm-dev/kimmdy/compare/v6.5.0...v6.6.0) (2024-04-25)
+
+
+### Features
+
+* add explicit includes and excludes for modify_top ([#427](https://github.com/hits-mbm-dev/kimmdy/issues/427)) ([c1318c3](https://github.com/hits-mbm-dev/kimmdy/commit/c1318c3d55bb21e6ee0e82e32301cc45ca8e7f24))
+* Expose grappa model and charge type ([#430](https://github.com/hits-mbm-dev/kimmdy/issues/430)) ([57af388](https://github.com/hits-mbm-dev/kimmdy/commit/57af38808dd510640cc53420803d2299f5e172f5))
+* modify top tut ([#428](https://github.com/hits-mbm-dev/kimmdy/issues/428)) ([823b7ff](https://github.com/hits-mbm-dev/kimmdy/commit/823b7ffe631c13501266804a90ecd11f8397886b))
+
+
+### Bug Fixes
+
+* handle time windows w/ no rates in extrande_mod correctly ([f5c3f7c](https://github.com/hits-mbm-dev/kimmdy/commit/f5c3f7c76f4c18a7e98cf2fe13afbe1c47041ead))
+* typo ([7130aff](https://github.com/hits-mbm-dev/kimmdy/commit/7130aff8f09dbe56231b1d2c20ee2b620db8aaca))
+
+
+### Documentation
+
+* how_to page for analysis ([#424](https://github.com/hits-mbm-dev/kimmdy/issues/424)) ([b35e1c8](https://github.com/hits-mbm-dev/kimmdy/commit/b35e1c86534dc59090150d2a94c912f9903f0c83))
+
 ## [6.5.0](https://github.com/hits-mbm-dev/kimmdy/compare/v6.4.1...v6.5.0) (2024-03-25)
 
 

docs/guide/explanation/index.html

@@ -555,15 +555,15 @@ <h1 class="title">Explanations</h1>
 </tr>
 </thead>
 <tbody class="list">
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+<tr data-index="0" data-listing-file-modified-sort="1714039452673" data-listing-reading-time-sort="20" 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="1714038932627" data-listing-reading-time-sort="1" data-listing-title-sort="Visualize Topologies" data-listing-filename-sort="topology.qmd">
+<tr data-index="1" data-listing-file-modified-sort="1714039452673" 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>

docs/guide/how-to/index.html

@@ -555,47 +555,47 @@ <h1 class="title">How-To</h1>
 </tr>
 </thead>
 <tbody class="list">
-<tr data-index="0" data-listing-file-modified-sort="1714038932631" data-listing-reading-time-sort="2" data-listing-title-sort="Analyze a KIMMDY run" data-listing-filename-sort="analyze.qmd">
+<tr data-index="0" data-listing-file-modified-sort="1714039452677" data-listing-reading-time-sort="2" 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>
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+<tr data-index="1" data-listing-file-modified-sort="1714039452677" data-listing-reading-time-sort="2" data-listing-title-sort="Contribute" data-listing-filename-sort="contribute.qmd">
 <td>
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 <span class="listing-author">&nbsp;</span>
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 <td>
 <a href="../../guide/how-to/examples.html" class="title listing-title">Examples</a>
 </td>
 <td>
 <span class="listing-author">&nbsp;</span>
 </td>
 </tr>
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+<tr data-index="3" data-listing-file-modified-sort="1714039452677" data-listing-reading-time-sort="1" data-listing-title-sort="High Performance Computing" data-listing-filename-sort="hcp.qmd">
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 <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="4" data-listing-file-modified-sort="1714038932631" 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="4" data-listing-file-modified-sort="1714039452677" 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="5" data-listing-file-modified-sort="1714038932631" 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="1714039452677" 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>

docs/guide/tutorials/getting-started.html

@@ -621,7 +621,7 @@ <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>
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+    molstar.Viewer.create("app-./getting-started-files/vis-ala.molj", {"viewportShowAnimation":true,"layoutShowLog":false,"layoutShowLeftPanel":true,"layoutShowControls":false,"layoutShowRemoteState":false,"layoutShowSequence":false,"viewportShowExpand":true,"layoutIsExpanded":false,"emdbProvider":"rcsb","pdbProvider":"rcsb","viewportShowSelectionMode":false}).then(viewer => {
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docs/guide/tutorials/index.html

@@ -525,7 +525,7 @@ <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="1714038932635" data-listing-reading-time-sort="3">
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 <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>
@@ -557,7 +557,7 @@ <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="1714038932639" data-listing-reading-time-sort="6">
+<div class="quarto-post image-right" data-index="1" data-categories="user" data-listing-file-modified-sort="1714039452685" data-listing-reading-time-sort="6">
 <div class="thumbnail">
 <p><a href="../../guide/tutorials/modify-topology.html"> <img src="../../guide/tutorials/img/getting-started-vmd-radicals.png" class="thumbnail-image"> </a></p>
 </div>
@@ -589,7 +589,7 @@ <h3 class="no-anchor listing-title">
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+<div class="quarto-post image-right" data-index="2" data-categories="user" data-listing-file-modified-sort="1714039452681" data-listing-reading-time-sort="6">
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 <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>

docs/guide/tutorials/modify-topology.html

@@ -613,7 +613,7 @@ <h1>Remove Hydrogens and parameterize for radical starting structures</h1>
 <h3 class="anchored" data-anchor-id="minimized-structure-of-native-peptide">Minimized structure of native peptide</h3>
     <div id="app-./modify-topology-files/minim.pdb" class="molstar-app"></div>
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-    molstar.Viewer.create("app-./modify-topology-files/minim.pdb", {"pdbProvider":"rcsb","layoutIsExpanded":false,"layoutShowSequence":false,"viewportShowSelectionMode":false,"layoutShowRemoteState":false,"emdbProvider":"rcsb","layoutShowControls":false,"viewportShowAnimation":true,"layoutShowLog":false,"layoutShowLeftPanel":true,"viewportShowExpand":true}).then(viewer => {
+    molstar.Viewer.create("app-./modify-topology-files/minim.pdb", {"emdbProvider":"rcsb","pdbProvider":"rcsb","layoutShowControls":false,"layoutShowLeftPanel":true,"viewportShowExpand":true,"viewportShowAnimation":true,"layoutIsExpanded":false,"layoutShowRemoteState":false,"layoutShowLog":false,"viewportShowSelectionMode":false,"layoutShowSequence":false}).then(viewer => {
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@@ -622,7 +622,7 @@ <h3 class="anchored" data-anchor-id="minimized-structure-of-native-peptide">Mini
 <h3 class="anchored" data-anchor-id="minimized-structure-with-deleted-hydrogen">Minimized structure with deleted hydrogen</h3>
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+    molstar.Viewer.create("app-./modify-topology-files/minim_delH.pdb", {"emdbProvider":"rcsb","pdbProvider":"rcsb","layoutShowControls":false,"layoutShowLeftPanel":true,"viewportShowExpand":true,"viewportShowAnimation":true,"layoutIsExpanded":false,"layoutShowRemoteState":false,"layoutShowLog":false,"viewportShowSelectionMode":false,"layoutShowSequence":false}).then(viewer => {
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