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BradyAJohnston · Nov 30, 2023 · 0c9abaa · 0c9abaa
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diff --git a/.nojekyll b/.nojekyll
@@ -0,0 +1 @@
+54bfb537
diff --git a/examples.html b/examples.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.358">
+<meta name="generator" content="quarto-1.4.449">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -81,7 +81,7 @@
   "collapse-after": 3,
   "panel-placement": "start",
   "type": "textbox",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
@@ -235,6 +235,7 @@ <h1 class="title">Examples</h1>
 
 </header>
 
+
 <section id="animating-atp-synthase" class="level2" data-number="1">
 <h2 data-number="1" class="anchored" data-anchor-id="animating-atp-synthase"><span class="header-section-number">1</span> Animating ATP Synthase</h2>
 <p><img src="https://github.com/BradyAJohnston/MolecularNodes/raw/main/img/atp-animation-demo.gif" class="img-fluid"></p>
@@ -605,15 +606,38 @@ <h3 data-number="2.4" class="anchored" data-anchor-id="geometry-nodes"><span cla
       }
     }
     stripColumnClz(note)
-    if (id.startsWith('sec-')) {
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
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+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
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@@ -622,6 +646,7 @@ <h3 data-number="2.4" class="anchored" data-anchor-id="geometry-nodes"><span cla
       if (anchorLink) {
         anchorLink.remove();
       }
+      typesetMath(note);
       return note.innerHTML;
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@@ -664,6 +689,29 @@ <h3 data-number="2.4" class="anchored" data-anchor-id="geometry-nodes"><span cla
             instance.show();
           });
         }
+      } else {
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
+        .then(res => res.text())
+        .then(html => {
+          const parser = new DOMParser();
+          const htmlDoc = parser.parseFromString(html, "text/html");
+          const note = htmlDoc.querySelector('main.content');
+          if (note !== null) {
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
+            instance.setContent(html);
+          } 
+        }).finally(() => {
+          instance.enable();
+          instance.show();
+        });
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@@ -739,7 +787,6 @@ <h3 data-number="2.4" class="anchored" data-anchor-id="geometry-nodes"><span cla
     window.addEventListener(
       "resize",
       throttle(() => {
-        console.log("RESIZE");
         elRect = undefined;
         if (selectedAnnoteEl) {
           selectCodeLines(selectedAnnoteEl);

diff --git a/index.html b/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.358">
+<meta name="generator" content="quarto-1.4.449">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -47,7 +47,7 @@
   "collapse-after": 3,
   "panel-placement": "start",
   "type": "textbox",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
@@ -192,6 +192,7 @@ <h1 class="title">About</h1>
 
 </header>
 
+
 <p>Molecular Nodes (MN) is an addon for the 3D modelling &amp; animation program <a href="https://blender.org">Blender</a>. MN enables easy import of molecular data such as <code>.pdb</code> &amp; <code>.mmCIF</code>, along with a variety of molecular dynamics trajectories and topologies from a variety of simulation sources. Other data formats including electron microscopy (EM) <code>.map</code>, EM tomography files such as <code>.map</code> and <code>.star</code>, with the potential to support more data formats as well.</p>
 <p>Molecular Nodes provides the translation layer that allows importing of molecular data formats, while Blender provides the industry-leading animation and rendering tools to create visually stunning molecular graphics with ease.</p>
 <p>The add-on runs on the <a href="https://docs.blender.org/manual/en/latest/modeling/geometry_nodes/introduction.html">Geometry Nodes</a> procedural modelling and animation system inside of Blender, which gives the add-on speed and robustness with minimal user input required.</p>
@@ -242,11 +243,7 @@ <h4 class="anchored" data-anchor-id="nano-rooms">Nano Rooms</h4>
 </section>
 <section id="st.-jude-childrens-research-hospital" class="level4">
 <h4 class="anchored" data-anchor-id="st.-jude-childrens-research-hospital">St.&nbsp;Jude Children’s Research Hospital</h4>
-<div class="quarto-figure quarto-figure-center">
-<figure class="figure">
-<p><a href="https://awards.ami.org/gallery/WOVQRGgD/LrVXNAor?search=848d592b94f65998-20"><img src="https://i.imgur.com/YpaJXEV.png" class="img-fluid figure-img" data-align="left"></a></p>
-</figure>
-</div>
+<p><a href="https://awards.ami.org/gallery/WOVQRGgD/LrVXNAor?search=848d592b94f65998-20"><img src="https://i.imgur.com/YpaJXEV.png" class="img-fluid" data-align="left"></a></p>
 </section>
 </section>
 <section id="getting-started" class="level2">
@@ -534,15 +531,38 @@ <h2 class="anchored" data-anchor-id="getting-started">Getting Started</h2>
       }
     }
     stripColumnClz(note)
-    if (id.startsWith('sec-')) {
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
         for (let i = 0; i < 2; i++) {
           container.appendChild(note.children[i].cloneNode(true));
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
@@ -551,6 +571,7 @@ <h2 class="anchored" data-anchor-id="getting-started">Getting Started</h2>
       if (anchorLink) {
         anchorLink.remove();
       }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -593,6 +614,29 @@ <h2 class="anchored" data-anchor-id="getting-started">Getting Started</h2>
             instance.show();
           });
         }
+      } else {
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
+        .then(res => res.text())
+        .then(html => {
+          const parser = new DOMParser();
+          const htmlDoc = parser.parseFromString(html, "text/html");
+          const note = htmlDoc.querySelector('main.content');
+          if (note !== null) {
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
+            instance.setContent(html);
+          } 
+        }).finally(() => {
+          instance.enable();
+          instance.show();
+        });
       }
     }, function(instance) {
     });
@@ -668,7 +712,6 @@ <h2 class="anchored" data-anchor-id="getting-started">Getting Started</h2>
     window.addEventListener(
       "resize",
       throttle(() => {
-        console.log("RESIZE");
         elRect = undefined;
         if (selectedAnnoteEl) {
           selectCodeLines(selectedAnnoteEl);

diff --git a/installation.html b/installation.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.358">
+<meta name="generator" content="quarto-1.4.449">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -81,7 +81,7 @@
   "collapse-after": 3,
   "panel-placement": "start",
   "type": "textbox",
-  "limit": 20,
+  "limit": 50,
   "keyboard-shortcut": [
     "f",
     "/",
@@ -238,13 +238,14 @@ <h1 class="title">Installation</h1>
 
 </header>
 
+
 <section id="downloading-blender" class="level2">
 <h2 class="anchored" data-anchor-id="downloading-blender">Downloading Blender</h2>
 <p>Molecular Nodes is an add-on for the 3D animation program Blender. It runs inside of Blender, so the first step for installation is to <a href="https://www.blender.org/download/">download and install</a> the latest version of blender.</p>
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure">
 <p><img src="images/installation/blender_download.png" class="img-fluid figure-img" data-align="center" width="800"></p>
-<figcaption class="figure-caption">The download page of Blender.</figcaption>
+<figcaption>The download page of Blender.</figcaption>
 </figure>
 </div>
 </section>
@@ -264,11 +265,7 @@ <h2 class="anchored" data-anchor-id="downloading-molecular-nodes">Downloading Mo
 <p>When downloading on MacOS with Safari, it automatically unzips the file into a <code>MolecularNodes</code> folder. This is extremely unhelpful as Blender requires the <code>.zip</code> file to install the addon. Either download with a different browser, or compress the folder again to <code>MolecularNodes.zip</code>.</p>
 </div>
 </div>
-<div class="quarto-figure quarto-figure-center">
-<figure class="figure">
-<p><a href="https://github.com/BradyAJohnston/MolecularNodes/releases/"><img src="images/installation/mn-download.png" class="img-fluid figure-img" alt="Screenshot of the Molecular Nodes releases page on Github, with the relevant download link circled in red."></a></p>
-</figure>
-</div>
+<p><a href="https://github.com/BradyAJohnston/MolecularNodes/releases/"><img src="images/installation/mn-download.png" class="img-fluid" alt="Screenshot of the Molecular Nodes releases page on Github, with the relevant download link circled in red."></a></p>
 </section>
 <section id="installing-the-addon" class="level2">
 <h2 class="anchored" data-anchor-id="installing-the-addon">Installing the Addon</h2>
@@ -633,15 +630,38 @@ <h1>Start Importing Structures!</h1>
       }
     }
     stripColumnClz(note)
-    if (id.startsWith('sec-')) {
+    const typesetMath = (el) => {
+      if (window.MathJax) {
+        // MathJax Typeset
+        window.MathJax.typeset([el]);
+      } else if (window.katex) {
+        // KaTeX Render
+        var mathElements = el.getElementsByClassName("math");
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            window.katex.render(texText.data, mathElements[i], {
+              displayMode: mathElements[i].classList.contains('display'),
+              throwOnError: false,
+              macros: macros,
+              fleqn: false
+            });
+          }
+        }
+      }
+    }
+    if (id === null || id.startsWith('sec-')) {
       // Special case sections, only their first couple elements
       const container = document.createElement("div");
       if (note.children && note.children.length > 2) {
         for (let i = 0; i < 2; i++) {
           container.appendChild(note.children[i].cloneNode(true));
         }
+        typesetMath(container);
         return container.innerHTML
       } else {
+        typesetMath(note);
         return note.innerHTML;
       }
     } else {
@@ -650,6 +670,7 @@ <h1>Start Importing Structures!</h1>
       if (anchorLink) {
         anchorLink.remove();
       }
+      typesetMath(note);
       return note.innerHTML;
     }
   }
@@ -692,6 +713,29 @@ <h1>Start Importing Structures!</h1>
             instance.show();
           });
         }
+      } else {
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
+        .then(res => res.text())
+        .then(html => {
+          const parser = new DOMParser();
+          const htmlDoc = parser.parseFromString(html, "text/html");
+          const note = htmlDoc.querySelector('main.content');
+          if (note !== null) {
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
+            instance.setContent(html);
+          } 
+        }).finally(() => {
+          instance.enable();
+          instance.show();
+        });
       }
     }, function(instance) {
     });
@@ -767,7 +811,6 @@ <h1>Start Importing Structures!</h1>
     window.addEventListener(
       "resize",
       throttle(() => {
-        console.log("RESIZE");
         elRect = undefined;
         if (selectedAnnoteEl) {
           selectCodeLines(selectedAnnoteEl);

diff --git a/robots.txt b/robots.txt
@@ -0,0 +1 @@
+Sitemap: https://BradyAJohnston.github.io/MolecularNodes/sitemap.xml