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201<div class="quarto-title">
202<h1 class="title">About</h1>
203</div>
204
205
206
207<div class="quarto-title-meta">
208
209    
210  
211    
212  </div>
213  
214
215
216</header>
217
218
219<p><img src="images/logo.png" align="right" style="height:250px;"></p>
220<p><img src="https://github.com/bradyajohnston/molecularnodes/actions/workflows/docs.yml/badge.svg" class="img-fluid" alt="Documentation Building"> <img src="https://github.com/bradyajohnston/molecularnodes/actions/workflows/tests.yml/badge.svg" class="img-fluid" alt="Running Tests"> <a href="https://codecov.io/gh/BradyAJohnston/MolecularNodes"><img src="https://codecov.io/gh/BradyAJohnston/MolecularNodes/branch/main/graph/badge.svg?token=ZB2SJFY8FU" class="img-fluid" alt="codecov"></a></p>
221<p><a href="https://www.github.com/bradyajohnston/MolecularNodes/releases"><img src="https://img.shields.io/github/v/release/bradyajohnston/molecularnodes" alt="Badge displaying license, which is MIT." style="height:20px"></a> <a href="https://www.github.com/bradyajohnston/MolecularNodes/releases"><img src="https://img.shields.io/github/downloads/BradyAJohnston/MolecularNodes/total.svg" alt="Repo total downloads count." style="height:20px"></a> <a href="https://www.buymeacoffee.com/bradyajohnston"><img src="https://img.shields.io/github/license/bradyajohnston/molecularnodes" alt="Badge displaying license, which is MIT." style="height:20px"></a> <a href="https://www.buymeacoffee.com/bradyajohnston"><img src="https://img.shields.io/github/stars/bradyajohnston/molecularnodes?style=social" alt="Badge displaying count of GitHub stars." style="height:20px"></a></p>
222<p><a href="https://pypi.org/project/biotite"><img src="https://img.shields.io/badge/powered%20by-Biotite-orange.svg" alt="Badge showing usage of MDAnalysis as a python package powering the add-on" style="height:20px"></a> <a href="https://pypi.org/project/MDAnalysis"><img src="https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg" alt="Badge showing usage of biotite as a python package powering the add-on" style="height:20px"></a></p>
223<p><a href="https://patreon.com/bradyajohnston"><img src="https://img.shields.io/endpoint.svg?url=https%3A%2F%2Fshieldsio-patreon.vercel.app%2Fapi%3Fusername%3Dbradyajohnston%26type%3Dpatrons&amp;style=for-the-badge" alt="Support me on Patreon with ongoing donations" style="height:35px"></a></p>
224<p><a href="https://buymeacoffee.com/bradyajohnston"><img src="https://img.shields.io/badge/Buy%20Me%20a%20Coffee-ffdd00?style=for-the-badge&amp;logo=buy-me-a-coffee&amp;logoColor=black" alt="Support me by buying a couple of coffees as a one-off donation" style="height:35px"></a></p>
225<p><a href="https://discord.gg/fvw6vT3vY9"><img src="https://img.shields.io/badge/Discord-%235865F2.svg?style=for-the-badge&amp;logo=discord&amp;logoColor=white" alt="Join the scientific visualisation in Blender discord." style="height:35px"></a></p>
226<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>
226.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>
227<p>See the talk below at the 2022 Blender conference for an overview of the add-on it’s capabilities.</p>
228<div class="center">
229<iframe width="560" height="315" src="https://www.youtube.com/embed/adhTmwYwOiA?si=em6xRime7HZ8L44T" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen="">
230</iframe>
231</div>
232<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>
233<p>The add-on runs on the <a href="https://docs.blender.org/manual/en/latest/modeling/geometry_nodes/introduction.html">
233Geometry Nodes</a> procedural modelling and animation system inside of Blender, which gives the add-on speed and robustness with minimal user input required.</p>
234<table class="caption-top table">
235<colgroup>
236<col style="width: 33%">
237<col style="width: 33%">
238<col style="width: 33%">
239</colgroup>
240<thead>
241<tr class="header">
242<th>Procedural Animations</th>
243<th>Different Stylings</th>
244<th>MD Trajectories</th>
245</tr>
246</thead>
247<tbody>
248<tr class="odd">
249<td><img src="images/index/mn-cartoon-example.gif" class="img-fluid" width="400"></td>
250<td><img src="images/index/mn-md-example-spike.gif" class="img-fluid"></td>
251<td><img src="images/index/mn-md-example.gif" class="img-fluid"></td>
252</tr>
253<tr class="even">
254<td>EM Density maps</td>
255<td><code>.star</code> mapbacks</td>
256<td></td>
257</tr>
258<tr class="odd">
259<td><img src="images/index/mn-example-em.gif" class="img-fluid"></td>
260<td><video src="images/index/mn-example-starfile.mp4" class="img-fluid" controls=""><a href="images/index/mn-example-starfile.mp4">Video</a></video></td>
261<td></td>
262</tr>
263</tbody>
264</table>
265<section id="getting-started" class="level2">
266<h2 class="anchored" data-anchor-id="getting-started">Getting Started</h2>
267<p>To get started, checkout the <a href="#installation">installation page</a> for detailed instructions on how to install the add-on. Next check out some of the tutorials, such as <a href="./tutorials/interface.html">intro to blender</a>, <a href="./tutorials/importing.html">basics of downloading</a> from the PDB or how to <a href="./tutorials/selections.html">customise selections</a>.</p>
268<p>There are some <em>outdated</em> tutorials on YouTube about how to use the add-on also. MN has been developed further and improved since these videos, but the general workflow remains the same.</p>
269<div class="center">
270<iframe width="560" height="315" src="https://www.youtube.com/embed/CvmFaRVmZRU" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="">
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273
274
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487              const parser = new DOMParser();
488              const htmlDoc = parser.parseFromString(html, "text/html");
489              const note = htmlDoc.getElementById(id);
490              if (note !== null) {
491                const html = processXRef(id, note);
492                instance.setContent(html);
493              } 
494            }).finally(() => {
495              instance.enable();
496              instance.show();
497            });
498          }
499        } else {
500          // See if we can fetch a full url (with no hash to target)
501          // This is a special case and we should probably do some content thinning / targeting
502          fetch(url)
503          .then(res => res.text())
504          .then(html => {
505            const parser = new DOMParser();
506            const htmlDoc = parser.parseFromString(html, "text/html");
507            const note = htmlDoc.querySelector('main.content');
508            if (note !== null) {
509              // This should only happen for chapter cross references
510              // (since there is no id in the URL)
511              // remove the first header
512              if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
513                note.children[0].remove();
514              }
515              const html = processXRef(null, note);
516              instance.setContent(html);
517            } 
518          }).finally(() => {
519            instance.enable();
520            instance.show();
521          });
522        }
523      }, function(instance) {
524      });
525    }
526        let selectedAnnoteEl;
527        const selectorForAnnotation = ( cell, annotation) => {
528          let cellAttr = 'data-code-cell="' + cell + '"';
529          let lineAttr = 'data-code-annotation="' +  annotation + '"';
530          const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
531          return selector;
532        }
533        const selectCodeLines = (annoteEl) => {
534          const doc = window.document;
535          const targetCell = annoteEl.getAttribute("data-target-cell");
536          const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
537          const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
538          const lines = annoteSpan.getAttribute("data-code-lines").split(",");
539          const lineIds = lines.map((line) => {
540            return targetCell + "-" + line;
541          })
542          let top = null;
543          let height = null;
544          let parent = null;
545          if (lineIds.length > 0) {
546              //compute the position of the single el (top and bottom and make a div)
547              const el = window.document.getElementById(lineIds[0]);
548              top = el.offsetTop;
549              height = el.offsetHeight;
550              parent = el.parentElement.parentElement;
551            if (lineIds.length > 1) {
552              const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
553              const bottom = lastEl.offsetTop + lastEl.offsetHeight;
554              height = bottom - top;
555            }
556            if (top !== null && height !== null && parent !== null) {
557              // cook up a div (if necessary) and position it 
558              let div = window.document.getElementById("code-annotation-line-highlight");
559              if (div === null) {
560                div = window.document.createElement("div");
561                div.setAttribute("id", "code-annotation-line-highlight");
562                div.style.position = 'absolute';
563                parent.appendChild(div);
564              }
565              div.style.top = top - 2 + "px";
566              div.style.height = height + 4 + "px";
567              div.style.left = 0;
568              let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
569              if (gutterDiv === null) {
570                gutterDiv = window.document.createElement("div");
571                gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
572                gutterDiv.style.position = 'absolute';
573                const codeCell = window.document.getElementById(targetCell);
574                const gutter = codeCell.querySelector('.code-annotation-gutter');
575                gutter.appendChild(gutterDiv);
576              }
577              gutterDiv.style.top = top - 2 + "px";
578              gutterDiv.style.height = height + 4 + "px";
579            }
580            selectedAnnoteEl = annoteEl;
581          }
582        };
583        const unselectCodeLines = () => {
584          const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
585          elementsIds.forEach((elId) => {
586            const div = window.document.getElementById(elId);
587            if (div) {
588              div.remove();
589            }
590          });
591          selectedAnnoteEl = undefined;
592        };
593          // Handle positioning of the toggle
594      window.addEventListener(
595        "resize",
596        throttle(() => {
597          elRect = undefined;
598          if (selectedAnnoteEl) {
599            selectCodeLines(selectedAnnoteEl);
600          }
601        }, 10)
602      );
603      function throttle(fn, ms) {
604      let throttle = false;
605      let timer;
606        return (...args) => {
607          if(!throttle) { // first call gets through
608              fn.apply(this, args);
609              throttle = true;
610          } else { // all the others get throttled
611              if(timer) clearTimeout(timer); // cancel #2
612              timer = setTimeout(() => {
613                fn.apply(this, args);
614                timer = throttle = false;
615              }, ms);
616          }
617        };
618      }
619        // Attach click handler to the DT
620        const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
621        for (const annoteDlNode of annoteDls) {
622          annoteDlNode.addEventListener('click', (event) => {
623            const clickedEl = event.target;
624            if (clickedEl !== selectedAnnoteEl) {
625              unselectCodeLines();
626              const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
627              if (activeEl) {
628                activeEl.classList.remove('code-annotation-active');
629              }
630              selectCodeLines(clickedEl);
631              clickedEl.classList.add('code-annotation-active');
632            } else {
633              // Unselect the line
634              unselectCodeLines();
635              clickedEl.classList.remove('code-annotation-active');
636            }
637          });
638        }
639    const findCites = (el) => {
640      const parentEl = el.parentElement;
641      if (parentEl) {
642        const cites = parentEl.dataset.cites;
643        if (cites) {
644          return {
645            el,
646            cites: cites.split(' ')
647          };
648        } else {
649          return findCites(el.parentElement)
650        }
651      } else {
652        return undefined;
653      }
654    };
655    var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
656    for (var i=0; i<bibliorefs.length; i++) {
657      const ref = bibliorefs[i];
658      const citeInfo = findCites(ref);
659      if (citeInfo) {
660        tippyHover(citeInfo.el, function() {
661          var popup = window.document.createElement('div');
662          citeInfo.cites.forEach(function(cite) {
663            var citeDiv = window.document.createElement('div');
664            citeDiv.classList.add('hanging-indent');
665            citeDiv.classList.add('csl-entry');
666            var biblioDiv = window.document.getElementById('ref-' + cite);
667            if (biblioDiv) {
668              citeDiv.innerHTML = biblioDiv.innerHTML;
669            }
670            popup.appendChild(citeDiv);
671          });
672          return popup.innerHTML;
673        });
674      }
675    }
676  });
677  </script>
677
678</div> <!-- /content -->
679<footer class="footer">
680  <div class="nav-footer">
681    <div class="nav-footer-left">
682<p>This site is built with ❤️ and <a href="https://quarto.org/">Quarto</a>.</p>
683</div>   
684    <div class="nav-footer-center">
685      &nbsp;
686    </div>
687    <div class="nav-footer-right">
688      &nbsp;
689    </div>
690  </div>
691</footer>
692
693
694
695
696</body></html>

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