Mercurial > repos > galaxy-australia > alphafold2

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    <title> Alphafold structure prediction </title>

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  </head>


  <body>
    <h1> Alphafold structure prediction </h1>

    <div class="main flex">
      <div class="col relative">
        <div id="ngl-root-parent">

          <div id="ngl-root"></div>

          <div id="ngl-nothing">
            Select a representation to display
          </div>

          <div id="ngl-loading">
            <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" style="margin: auto; background: none; display: block; shape-rendering: auto;" width="200px" height="200px" viewBox="0 0 100 100" preserveAspectRatio="xMidYMid">
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                <rect x="47" y="24" rx="3" ry="6" width="6" height="12" fill="#88879e">
                  <animate attributeName="opacity" values="1;0" keyTimes="0;1" dur="1s" begin="-0.9166666666666666s" repeatCount="indefinite"></animate>
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        </div>

        <div class="flex">
          <div class="box space-1">
            <p>
              <span class="mono">Scroll up/down</span>
              to zoom in and out
            </p>
            <p>
              <span class="mono">Click + drag</span>
              to rotate the structure
            </p>
            <p>
              <span class="mono">CTRL + click + drag</span>
              to move the structure
            </p>
            <p>
              <span class="mono">Click</span>
              an atom to bring it into focus
            </p>
          </div>

          <div class="box legend">
            <div class="scale">
              <div class="color"></div>
              <div class="flex ticks">
                <div>&lt;50</div>
                <div>70</div>
                <div>90+</div>
              </div>
            </div>

            <div>
              <p class="text-center">
                <small>
                Alphafold produces a
                <a href="https://alphafold.ebi.ac.uk/faq#faq-5" target="_blank">
                  per-residue confidence score (pLDDT)
                </a>
                between 0 and 100. Some regions below 50 pLDDT may be
                unstructured in isolation.
              </small>
              </p>
            </div>
          </div>
        </div>
      </div>

      <div class="flex col controls">
        <div class="box text-center">
          <h3> Select model </h3>
          <p>The top five structures predicted by Alphafold</p>
          <div>
            <button class="btn selected" id="btn-ranked_0" onclick="setModel(0);">
              Model 1
            </button>

            <button class="btn" id="btn-ranked_1" onclick="setModel(1);">
              Model 2
            </button>

            <button class="btn" id="btn-ranked_2" onclick="setModel(2);">
              Model 3
            </button>

            <button class="btn" id="btn-ranked_3" onclick="setModel(3);">
              Model 4
            </button>

            <button class="btn" id="btn-ranked_4" onclick="setModel(4);">
              Model 5
            </button>
          </div>
        </div>

        <div class="box text-center">
          <h3> Toggle representations </h3>
          <div>
            <button class="btn selected" id="btn-cartoon" onclick="toggleModelRepresentation('cartoon');">
              Cartoon
            </button>

            <button class="btn" id="btn-ball-stick" onclick="toggleModelRepresentation('ball+stick');">
              Ball + stick
            </button>

            <button class="btn" id="btn-surface" onclick="toggleModelRepresentation('surface');">
              Surface
            </button>

            <button class="btn" id="btn-backbone" onclick="toggleModelRepresentation('backbone');">
              Backbone
            </button>
          </div>
        </div>

        <div class="box text-center">
          <h3> Actions </h3>
          <div>
            <button class="btn selected" id="btn-toggle-spin" onclick="toggleSpin();">
              Toggle spin
            </button>

            <button class="btn" id="btn-toggle-dark" onclick="toggleDark();">
              Dark mode
            </button>
          </div>
        </div>

        <div class="box text-center">
          <h3> Download </h3>
          <div>
            <button class="btn green" onclick="downloadPng();">
              Snapshot
            </button>

            <button class="btn green" onclick="downloadPdb();">
              PDB
            </button>
          </div>
        </div>
      </div>
    </div>
  </body>


  <script type="text/javascript">

    // Render NGLviewer for PDB files

    // State management has been implemented with vanilla Js but could have used
    // Vue - it's a fairly simple use case so a global 'state' object works fine
    // without complicating things too much.


    // Define a custom color scheme to represent model confidence consistently
    // across different representations
    // ------------------------------------------------------------------------
    const colorScale = chroma.scale([
      'red', 'yellow', 'green', 'cyan', 'blue'
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      'ranked_4.pdb',
    ]

    const REPRESENTATIONS = [
      'cartoon',
      'ball+stick',
      'surface',
      'backbone',
    ]

    const DEFAULT_REPRESENTATION = REPRESENTATIONS[0];
    const MAX_CLICK_INTERVAL_MS = 500;  // For debouncing model clicks

    let stage;
    let nonceSetModel;

    let state = {
      model: 0,
      modelObject: null,
      representations: {},
      colorScheme: 'bfactor',
      darkMode: false,
      loading: 1,
      spin: true,
    }

    const uri = (i) => MODELS[i];
    // Switch to this function to return sample model URI (local dev)
    // const uri = (i) => `https://raw.githubusercontent.com/neoformit/alphafold-galaxy/main/data/${MODELS[i]}`;

    document.addEventListener("DOMContentLoaded", async function () {
      // Can set debug for development if NGL is being... funny
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      // Create NGL Stage object
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      // Handle window resizing
      window.addEventListener("resize",  () => stage.handleResize());

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    // Models ------------------------------------------------------------------

    const setModel = (ix) => {
      state.model = ix;
      stage.removeComponent(state.modelObject);
      setLoading(1);

      // Debounce rapid model clicking with a nonce
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      const localNonce = nonceSetModel;
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        state.representations = {};
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      // Load PDB entry
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        state.modelObject = o;
        reps.forEach( (r) => addModelRepresentation(r) );
        stage.setSpin(state.spin);
        o.autoView();
        setLoading(0);
      })
    }

    // Representations ---------------------------------------------------------

    const toggleModelRepresentation = (rep) => {
      rep in state.representations ?
        removeModelRepresentation(rep)
        : addModelRepresentation(rep)
    }

    const addModelRepresentation = (rep) => {
      state.representations[rep] =
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      updateButtons();
    }

    const removeModelRepresentation = (rep) => {
      o = state.representations[rep];
      state.modelObject.removeRepresentation(o);
      delete state.representations[rep];
      updateButtons();
    }

    const clearModelRepresentations = () => {
      state.modelObject && state.modelObject.removeAllRepresentations();
      state.representations = {};
    }

    // Actions -----------------------------------------------------------------

    const toggleDark = () => {
      state.darkMode = !state.darkMode;
      stage.setParameters({
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      const btn = document.querySelector('#btn-toggle-dark');
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        .style.display = state ? 'flex' : 'none';
      state.loading = state;
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      stage.toggleSpin();
      const btn = document.querySelector('#btn-toggle-spin');
      btn && btn.classList.toggle('selected');
      state.spin = !state.spin;
    }

    const downloadPng = () => {
      const params = {
        factor: 3,
        antialias: true,
      }
      stage.makeImage(params).then( (blob) => {
        const name = MODELS[state.model].replace('.pdb', '.png');
        const url = URL.createObjectURL(blob);
        makeDownload(url, name);
      })
    }

    const downloadPdb = () => {
      const url = uri(state.model);
      const name = `alphafold_${MODELS[state.model]}`;
      makeDownload(url, name);
    }

    const makeDownload = (url, name) => {
      // Will not work with cross-origin urls (i.e. during development)
      console.log(`Creating file download for ${name}, href ${url}`);
      const saveLink = document.createElement('a');
      saveLink.href = url;
      saveLink.download = name;
      document.body.appendChild(saveLink);
      saveLink.dispatchEvent(
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          bubbles: true,
          cancelable: true,
          view: window
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        if (name in state.representations) {
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        } else {
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</html>
author	galaxy-australia
date	Thu, 10 Mar 2022 21:53:42 +0000
parents	7ae9d78b06f5
children	d00e15139065