build based on 81b0e69

Author: Documenter.jl

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.12.5","generation_timestamp":"2026-02-16T05:25:17","documenter_version":"1.16.1"}}
+{"documenter":{"julia_version":"1.12.5","generation_timestamp":"2026-02-23T05:24:04","documenter_version":"1.17.0"}}

dev/api/index.html

@@ -37,7 +37,40 @@ function maybeAddWarning() {
   closer.addEventListener("click", function () {
     document.body.removeChild(div);
   });
-  const href = window.documenterBaseURL + "/../" + window.DOCUMENTER_STABLE;
+  var target_href =
+    window.documenterBaseURL + "/../" + window.DOCUMENTER_STABLE;
+
+  // try to stay on the same page when linking to the stable version
+  // get the current page path relative to the version root
+  var current_page = window.location.pathname;
+
+  // resolve the documenterBaseURL to an absolute path
+  // documenterBaseURL is a relative path (usually "."), so we need to resolve it
+  var base_url_absolute = new URL(documenterBaseURL, window.location.href)
+    .pathname;
+  if (!base_url_absolute.endsWith("/")) {
+    base_url_absolute = base_url_absolute + "/";
+  }
+
+  // extract the page path after the version directory
+  // e.g., if we're on /stable/man/guide.html, we want "man/guide.html"
+  var page_path = "";
+  if (current_page.startsWith(base_url_absolute)) {
+    page_path = current_page.substring(base_url_absolute.length);
+  }
+
+  // construct the target URL with the same page path
+  var target_url = target_href;
+  if (page_path && page_path !== "" && page_path !== "index.html") {
+    // ensure target_href ends with a slash before appending page path
+    if (!target_url.endsWith("/")) {
+      target_url = target_url + "/";
+    }
+    target_url = target_url + page_path;
+  }
+
+  // preserve the anchor (hash) from the current page
+  var current_hash = window.location.hash;
 
   // Determine if this is a development version or an older release
   let warningMessage = "";
@@ -51,12 +84,35 @@ function maybeAddWarning() {
       "This documentation is for an <strong>older version</strong> that may be missing recent changes.<br>";
   }
 
-  warningMessage +=
-    '<a href="' +
-    href +
-    '">Click here to go to the documentation for the latest stable release.</a>';
+  // Create the link element with same-page navigation
+  const link = document.createElement("a");
+  link.href = target_url + current_hash;
+  link.textContent =
+    "Click here to go to the documentation for the latest stable release.";
+
+  // If we're trying to stay on the same page, verify it exists first
+  if (page_path && page_path !== "" && page_path !== "index.html") {
+    link.addEventListener("click", function (e) {
+      e.preventDefault();
+      // check if the target page exists, fallback to homepage if it doesn't
+      fetch(target_url, { method: "HEAD" })
+        .then(function (response) {
+          if (response.ok) {
+            window.location.href = target_url + current_hash;
+          } else {
+            // page doesn't exist in the target version, go to homepage
+            window.location.href = target_href;
+          }
+        })
+        .catch(function (error) {
+          // network error or other failure - use homepage
+          window.location.href = target_href;
+        });
+    });
+  }
 
   div.innerHTML = warningMessage;
+  div.appendChild(link);
   div.appendChild(closer);
   document.body.appendChild(div);
 }

dev/assets/documenter.js

@@ -3502,4 +3502,4 @@
 ATOM      2  N   GLY A   1      25.020  38.731  48.032  1.00  0.00           N  </code></pre><p>leads to the error</p><pre><code class="nohighlight hljs">ERROR: Two copies of the same atom have the same alternative location ID. Existing atom:
 Atom N with serial 1, coordinates [25.776, 38.291, 47.527]
 New atom record to add:
-AtomRecord N with serial 2, coordinates [25.02, 38.731, 48.032]</code></pre><p>Such files often lead to silent errors, however, so we recommend that users follow the appropriate format guidelines. Alternatively, other tools such as <a href="https://github.com/m3g/PDBTools.jl">PDBTools.jl</a> are more permissive in what they accept. The mmCIF format is able to store arbitrary data systematically if required.</p><h2 id="Related-software"><a class="docs-heading-anchor" href="#Related-software">Related software</a><a id="Related-software-1"></a><a class="docs-heading-anchor-permalink" href="#Related-software" title="Permalink"></a></h2><p>Other packages in the Julia ecosystem that deal with structural bioinformatics or related fields include:</p><ul><li><a href="https://github.com/diegozea/MIToS.jl">MIToS.jl</a> - protein sequence and structure analysis.</li><li><a href="https://github.com/m3g/PDBTools.jl">PDBTools.jl</a> - read and write PDB files.</li><li><a href="https://github.com/christophfeinauer/PdbTool.jl">PdbTool.jl</a> - read and work with PDB files.</li><li><a href="https://github.com/chemfiles/Chemfiles.jl">Chemfiles.jl</a> - read and write various chemistry trajectory files.</li><li><a href="https://github.com/jgreener64/Bio3DView.jl">Bio3DView.jl</a> - view molecular structures (see <a href="#Visualising-structures">Visualising structures</a>).</li><li><a href="https://github.com/BioJulia/BioMakie.jl">BioMakie.jl</a> - view molecular structures and sequence alignments.</li><li><a href="https://github.com/MurrellGroup/ProtPlot.jl">ProtPlot.jl</a> - view protein ribbons with Makie.jl.</li><li><a href="https://github.com/m3g/ProteinSecondaryStructures.jl">ProteinSecondaryStructures.jl</a> - parses DSSP and STRIDE outputs.</li><li><a href="https://github.com/BioJulia/MMTF.jl">MMTF.jl</a> - read and write MMTF files. BioStructures.jl builds on top of MMTF.jl.</li><li><a href="https://github.com/jgreener64/ProteinEnsembles.jl">ProteinEnsembles.jl</a> - model ensembles of protein structures.</li><li><a href="https://github.com/jgreener64/Molly.jl">Molly.jl</a> - molecular dynamics in Julia.</li></ul></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../examples/">Examples »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.16.1 on <span class="colophon-date" title="Monday 16 February 2026 05:25">Monday 16 February 2026</span>. Using Julia version 1.12.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+AtomRecord N with serial 2, coordinates [25.02, 38.731, 48.032]</code></pre><p>Such files often lead to silent errors, however, so we recommend that users follow the appropriate format guidelines. Alternatively, other tools such as <a href="https://github.com/m3g/PDBTools.jl">PDBTools.jl</a> are more permissive in what they accept. The mmCIF format is able to store arbitrary data systematically if required.</p><h2 id="Related-software"><a class="docs-heading-anchor" href="#Related-software">Related software</a><a id="Related-software-1"></a><a class="docs-heading-anchor-permalink" href="#Related-software" title="Permalink"></a></h2><p>Other packages in the Julia ecosystem that deal with structural bioinformatics or related fields include:</p><ul><li><a href="https://github.com/diegozea/MIToS.jl">MIToS.jl</a> - protein sequence and structure analysis.</li><li><a href="https://github.com/m3g/PDBTools.jl">PDBTools.jl</a> - read and write PDB files.</li><li><a href="https://github.com/christophfeinauer/PdbTool.jl">PdbTool.jl</a> - read and work with PDB files.</li><li><a href="https://github.com/chemfiles/Chemfiles.jl">Chemfiles.jl</a> - read and write various chemistry trajectory files.</li><li><a href="https://github.com/jgreener64/Bio3DView.jl">Bio3DView.jl</a> - view molecular structures (see <a href="#Visualising-structures">Visualising structures</a>).</li><li><a href="https://github.com/BioJulia/BioMakie.jl">BioMakie.jl</a> - view molecular structures and sequence alignments.</li><li><a href="https://github.com/MurrellGroup/ProtPlot.jl">ProtPlot.jl</a> - view protein ribbons with Makie.jl.</li><li><a href="https://github.com/m3g/ProteinSecondaryStructures.jl">ProteinSecondaryStructures.jl</a> - parses DSSP and STRIDE outputs.</li><li><a href="https://github.com/BioJulia/MMTF.jl">MMTF.jl</a> - read and write MMTF files. BioStructures.jl builds on top of MMTF.jl.</li><li><a href="https://github.com/jgreener64/ProteinEnsembles.jl">ProteinEnsembles.jl</a> - model ensembles of protein structures.</li><li><a href="https://github.com/jgreener64/Molly.jl">Molly.jl</a> - molecular dynamics in Julia.</li></ul></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../examples/">Examples »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.17.0 on <span class="colophon-date" title="Monday 23 February 2026 05:24">Monday 23 February 2026</span>. Using Julia version 1.12.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/assets/warner.js

@@ -77,4 +77,4 @@
 fp = download("https://alphafold.ebi.ac.uk/files/AF-P24941-F1-model_v4.pdb")
 struc = read(fp, PDBFormat; run_dssp=true)
 sscodes = sscode.(collectresidues(struc))
-println(join(sscodes))</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../documentation/">« Documentation</a><a class="docs-footer-nextpage" href="../api/">API »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.16.1 on <span class="colophon-date" title="Monday 16 February 2026 05:25">Monday 16 February 2026</span>. Using Julia version 1.12.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+println(join(sscodes))</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../documentation/">« Documentation</a><a class="docs-footer-nextpage" href="../api/">API »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.17.0 on <span class="colophon-date" title="Monday 23 February 2026 05:24">Monday 23 February 2026</span>. Using Julia version 1.12.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>