fast docs interlinks

_quarto.yml

@@ -7,7 +7,7 @@ project:
     - _reference
     - guide
   resources:
-    - objects.json
+    - objects.txt
 
 
 website:
@@ -113,6 +113,7 @@ filters:
   - interlinks
 
 interlinks:
+  fast: true
   sources:
     numpy:
       url: https://numpy.org/doc/stable/

docs/guide/how-to/analyze.html

@@ -1141,7 +1141,7 @@ <h2 class="anchored" data-anchor-id="runtimes">Runtimes</h2>
   </div>
 </nav>
 </div> <!-- /content -->
-<footer class="footer"><div class="nav-footer"><div class="nav-footer-center"><div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/graeter-group/kimmdy/edit/main/guide/how-to/analyze.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/graeter-group/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div></div></footer><script>var lightboxQuarto = GLightbox({"loop":false,"openEffect":"zoom","closeEffect":"zoom","selector":".lightbox","descPosition":"bottom"});
+<footer class="footer"><div class="nav-footer"><div class="nav-footer-center"><div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/graeter-group/kimmdy/edit/main/guide/how-to/analyze.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/graeter-group/kimmdy/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div></div></footer><script>var lightboxQuarto = GLightbox({"descPosition":"bottom","openEffect":"zoom","closeEffect":"zoom","selector":".lightbox","loop":false});
 (function() {
   let previousOnload = window.onload;
   window.onload = () => {

docs/guide/tutorials/getting-started.html

@@ -625,7 +625,7 @@ <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", {"emdbProvider":"rcsb","layoutShowLog":false,"layoutIsExpanded":false,"viewportShowAnimation":true,"pdbProvider":"rcsb","layoutShowControls":false,"layoutShowRemoteState":false,"layoutShowSequence":false,"layoutShowLeftPanel":true,"viewportShowExpand":true,"viewportShowSelectionMode":false}).then(viewer => {
+    molstar.Viewer.create("app-./getting-started-files/vis-ala.molj", {"layoutIsExpanded":false,"layoutShowLog":false,"viewportShowSelectionMode":false,"layoutShowRemoteState":false,"emdbProvider":"rcsb","viewportShowExpand":true,"viewportShowAnimation":true,"layoutShowSequence":false,"layoutShowLeftPanel":true,"pdbProvider":"rcsb","layoutShowControls":false}).then(viewer => {
     viewer.loadSnapshotFromUrl(url="./getting-started-files/vis-ala.molj", "molj");    });
     </script>
 

docs/guide/tutorials/modify-topology.html

@@ -617,7 +617,7 @@ <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>
     <script type="text/javascript">
-    molstar.Viewer.create("app-./modify-topology-files/minim.pdb", {"emdbProvider":"rcsb","viewportShowAnimation":true,"layoutShowSequence":false,"viewportShowExpand":true,"layoutShowLeftPanel":true,"layoutIsExpanded":false,"layoutShowControls":false,"pdbProvider":"rcsb","viewportShowSelectionMode":false,"layoutShowLog":false,"layoutShowRemoteState":false}).then(viewer => {
+    molstar.Viewer.create("app-./modify-topology-files/minim.pdb", {"viewportShowSelectionMode":false,"layoutShowLog":false,"layoutShowRemoteState":false,"layoutShowSequence":false,"emdbProvider":"rcsb","layoutShowControls":false,"layoutShowLeftPanel":true,"viewportShowExpand":true,"layoutIsExpanded":false,"pdbProvider":"rcsb","viewportShowAnimation":true}).then(viewer => {
     viewer.loadStructureFromUrl("./modify-topology-files/minim.pdb", format="pdb");    });
     </script>
 
@@ -626,7 +626,7 @@ <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>
     <div id="app-./modify-topology-files/minim_delH.pdb" class="molstar-app"></div>
     <script type="text/javascript">
-    molstar.Viewer.create("app-./modify-topology-files/minim_delH.pdb", {"emdbProvider":"rcsb","viewportShowAnimation":true,"layoutShowSequence":false,"viewportShowExpand":true,"layoutShowLeftPanel":true,"layoutIsExpanded":false,"layoutShowControls":false,"pdbProvider":"rcsb","viewportShowSelectionMode":false,"layoutShowLog":false,"layoutShowRemoteState":false}).then(viewer => {
+    molstar.Viewer.create("app-./modify-topology-files/minim_delH.pdb", {"viewportShowSelectionMode":false,"layoutShowLog":false,"layoutShowRemoteState":false,"layoutShowSequence":false,"emdbProvider":"rcsb","layoutShowControls":false,"layoutShowLeftPanel":true,"viewportShowExpand":true,"layoutIsExpanded":false,"pdbProvider":"rcsb","viewportShowAnimation":true}).then(viewer => {
     viewer.loadStructureFromUrl("./modify-topology-files/minim_delH.pdb", format="pdb");    });
     </script>