@ccp-nc/crystvis-js 0.6.0 → 0.7.0

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Files changed (51) hide show
  1. package/.github/dependabot.yml +69 -0
  2. package/.github/workflows/dependency-review.yml +91 -0
  3. package/.github/workflows/security-scan.yml +113 -0
  4. package/.github/workflows/test.yml +191 -0
  5. package/.github/workflows/update-dependencies.yml +214 -0
  6. package/.mocharc.yml +4 -0
  7. package/.vscode/settings.json +5 -1
  8. package/CHANGELOG.md +61 -14
  9. package/README.md +75 -2
  10. package/audit.txt +24 -0
  11. package/changes.txt +2 -0
  12. package/demo/demo.css +15 -10
  13. package/demo/index.html +32 -5
  14. package/demo/main.js +149 -42
  15. package/docs/data/search.json +1 -1
  16. package/docs/index.html +51 -2
  17. package/docs/lib_model.module_js-AtomImage.html +1 -1
  18. package/docs/lib_model.module_js-BondImage.html +1 -1
  19. package/docs/lib_model.module_js-Model.html +1 -1
  20. package/docs/lib_modelview.module_js-ModelView.html +1 -1
  21. package/docs/lib_visualizer.module_js-CrystVis.html +1 -1
  22. package/docs/model.js.html +31 -3
  23. package/docs/modelview.js.html +24 -0
  24. package/docs/visualizer.js.html +237 -1
  25. package/eslint.config.js +41 -0
  26. package/lib/assets/fonts/threebmfont.js +0 -1
  27. package/lib/formats/magres.js +156 -1
  28. package/lib/formats/xyz.js +149 -52
  29. package/lib/loader.js +28 -7
  30. package/lib/model.js +31 -3
  31. package/lib/modelview.js +24 -0
  32. package/lib/primitives/ellipsoid.js +0 -4
  33. package/lib/primitives/geometries.js +0 -0
  34. package/lib/primitives/isosurface.js +1 -4
  35. package/lib/query.js +3 -28
  36. package/lib/render.js +97 -2
  37. package/lib/selbox.js +18 -4
  38. package/lib/tensor.js +0 -1
  39. package/lib/visualizer.js +237 -1
  40. package/outdated.txt +9 -0
  41. package/package.json +15 -15
  42. package/test/data/ethanol_with_tensors.xyz +33 -0
  43. package/test/data/hf_mu_test.magres +62 -0
  44. package/test/data/hf_test.magres +61 -0
  45. package/test/data/optimized_muon_65-hf.magres +1424 -0
  46. package/test/loader.js +283 -9
  47. package/test/model.js +120 -4
  48. package/test/setup-dom.cjs +147 -0
  49. package/test/visualizer.js +475 -0
  50. package/.eslintrc.json +0 -16
  51. package/.github/workflows/test-mocha.yml +0 -30
package/docs/lib_visualizer.module_js-CrystVis.html CHANGED
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7h18v2H3v-2zm0 7h18v2H3v-2z"/></symbol></defs></svg></head><body data-theme="dark"><div class="sidebar-container"><div class="sidebar" id="sidebar"><div class="sidebar-items-container"><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-modules"><div>Modules</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="lib_model.module_js.html">lib/model.js</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js.html">lib/modelview.js</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js.html">lib/visualizer.js</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-classes"><div>Classes</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="lib_model.module_js-AtomImage.html">AtomImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-BondImage.html">BondImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-Model.html">Model</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js-ModelView.html">ModelView</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js-CrystVis.html">CrystVis</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-tutorials"><div>Tutorials</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="tutorial-Events.html">Events</a></div><div class="sidebar-section-children"><a href="tutorial-Queries.html">Queries</a></div><div class="sidebar-section-children"><a href="tutorial-ThreejsMigration.html">ThreejsMigration</a></div></div></div></div></div><div class="navbar-container" id="VuAckcnZhf"><nav class="navbar"><div class="navbar-left-items"></div><div class="navbar-right-items"><div class="navbar-right-item"><button class="icon-button search-button" aria-label="open-search"><svg><use xlink:href="#search-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button theme-toggle" aria-label="toggle-theme"><svg><use class="theme-svg-use" xlink:href="#light-theme-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button font-size" aria-label="change-font-size"><svg><use xlink:href="#font-size-icon"></use></svg></button></div></div><nav></nav></nav></div><div class="toc-container"><div class="toc-content"><span class="bold">On this page</span><div id="eed4d2a0bfd64539bb9df78095dec881"></div></div></div><div class="body-wrapper"><div class="main-content"><div class="main-wrapper"><section><header><h1 id="CrystVis-title" class="has-anchor"><span class="ancestors"><a href="lib_visualizer.module_js.html">lib/visualizer.js</a>~</span> CrystVis</h1><div class="class-description"><p>An object providing a full interface to a renderer for crystallographic models</p></div></header><article><div class="container-overview"><h2 id="constructor" class="has-anchor">Constructor</h2><h3 class="name has-anchor" id="CrystVis"><span class="type-signature"></span>new CrystVis<span class="signature">(element, width, height, rendererOptions)</span></h3><div class="description"><p>An object providing a full interface to a renderer for crystallographic models</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>element</code></td><td class="type"><span class="param-type">string</span></td><td class="default"></td><td class="description last"><p>CSS-style identifier for the HTML element to put the renderer in</p></td></tr><tr><td class="name"><code>width</code></td><td class="type"><span class="param-type">int</span></td><td class="default">0</td><td class="description last"><p>Window width</p></td></tr><tr><td class="name"><code>height</code></td><td class="type"><span class="param-type">int</span></td><td class="default">0</td><td class="description last"><p>Window height. If both this and width are set to 0, the window fits its context and automatically resizes with it</p></td></tr><tr><td class="name"><code>rendererOptions</code></td><td class="type"><span class="param-type">Object</span></td><td class="default"></td><td class="description last"><p>Options for the renderer</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line38">line 38</a></li></ul></dd></div></dl></div><h2 id="members" class="subsection-title has-anchor">Members</h2><h3 class="name has-anchor" id="displayed"><span class="type-signature"></span>displayed<span class="type-signature"> :ModelView</span></h3><div class="description"><p>Displayed atoms</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">ModelView</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line121">line 121</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="highlightSelected"><span class="type-signature"></span>highlightSelected<span class="type-signature"> :bool</span></h3><div class="description"><p>Whether the selected atoms should be highlighted with auras</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">bool</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line154">line 154</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="model"><span class="type-signature">(readonly) </span>model<span class="type-signature"> :Model</span></h3><div class="description"><p>Currently loaded model</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Model</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line104">line 104</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="modelList"><span class="type-signature">(readonly) </span>modelList<span class="type-signature"> :Array</span></h3><div class="description"><p>List of loaded models</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line95">line 95</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="modelName"><span class="type-signature">(readonly) </span>modelName<span class="type-signature"> :String</span></h3><div class="description"><p>Name of the currently loaded model</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">String</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line113">line 113</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="selected"><span class="type-signature"></span>selected<span class="type-signature"> :ModelView</span></h3><div class="description"><p>Selected atoms</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">ModelView</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line138">line 138</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="theme"><span class="type-signature"></span>theme<span class="type-signature"> :object</span></h3><div class="description"><p>Theme</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">object</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line177">line 177</a></li></ul></dd></div></dl><h2 id="methods" class="subsection-title has-anchor">Methods</h2><h3 class="name has-anchor" id="addNotification"><span class="type-signature"></span>addNotification<span class="signature">()</span></h3><div class="description"><p>Add a notification to the list of notifications to be displayed</p></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line508">line 508</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="addNotifications"><span class="type-signature"></span>addNotifications<span class="signature">()</span></h3><div class="description"><p>Adds all notifications to the drawing</p></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line517">line 517</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="addPrimitive"><span class="type-signature"></span>addPrimitive<span class="signature">(p)</span></h3><div class="description"><p>Add a primitive shape to the drawing</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>p</code></td><td class="type"><span class="param-type">THREE.<wbr>Object3D</span></td><td class="description last"><p>Primitive to add</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line492">line 492</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="centerCamera"><span class="type-signature"></span>centerCamera<span class="signature">(center, shift)</span></h3><div class="description"><p>Center the camera on a given point</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>center</code></td><td class="type"><span class="param-type">Array.&lt;float></span></td><td class="description last"><p>Point in model space that the orbiting camera should be centred on and look at</p></td></tr><tr><td class="name"><code>shift</code></td><td class="type"><span class="param-type">Array.&lt;float></span></td><td class="description last"><p>Shift (in units of width/height of the canvas) with which the center of the camera should be rendered with respect to the center of the canvas</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line318">line 318</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="clearNotifications"><span class="type-signature"></span>clearNotifications<span class="signature">()</span></h3><div class="description"><p>Removes notifications from the drawing</p></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line528">line 528</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="deleteModel"><span class="type-signature"></span>deleteModel<span class="signature">(name)</span></h3><div class="description"><p>Erase a model from the recorded ones</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="description last"><p>Name of the model to delete</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line474">line 474</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="displayModel"><span class="type-signature"></span>displayModel<span class="signature">(name)</span></h3><div class="description"><p>Render a model</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="default">null</td><td class="description last"><p>Name of the model to display. If empty, just clear the renderer window.</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line424">line 424</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="getScreenshotData"><span class="type-signature"></span>getScreenshotData<span class="signature">()</span><span class="type-signature"> &rarr; {String}</span></h3><div class="description"><p>Recover a data URL of a PNG screenshot of the current scene</p></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line538">line 538</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>A data URL of the PNG screenshot</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">String</span></dd></dl></div><h3 class="name has-anchor" id="loadModels"><span class="type-signature"></span>loadModels<span class="signature">(contents, format, prefix, parameters)</span><span class="type-signature"> &rarr; {Object}</span></h3><div class="description"><p>Load one or more atomic models from a file's contents</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>contents</code></td><td class="type"><span class="param-type">String</span></td><td class="default"></td><td class="description last"><p>The contents of the structure file</p></td></tr><tr><td class="name"><code>format</code></td><td class="type"><span class="param-type">String</span></td><td class="default">cif</td><td class="description last"><p>The file's format (cif, xyz, etc.). Default is cif.</p></td></tr><tr><td class="name"><code>prefix</code></td><td class="type"><span class="param-type">String</span></td><td class="default">null</td><td class="description last"><p>Prefix to use when naming the models. Default is empty.</p></td></tr><tr><td class="name"><code>parameters</code></td><td class="type"><span class="param-type">Object</span></td><td class="default"></td><td class="description last"><p>Loading parameters:</p><ul><li><code>supercell</code>: supercell size (only used if the structure is periodic)</li><li><code>molecularCrystal</code>: if true, try to make the model load completing molecules across periodic boundaries</li><li><code>useNMRActiveIsotopes</code>: if true, all isotopes are set by default to the most common one with non-zero spin</li><li><code>vdwScaling</code>: scale van der Waals radii by a constant factor</li><li><code>vdwElementScaling</code>: table of per-element factors to scale VdW radii by</li></ul></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line341">line 341</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Names of the models we tried to load, and values of true/false for successful loading or not</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">Object</span></dd></dl></div><h3 class="name has-anchor" id="onAtomBox"><span class="type-signature"></span>onAtomBox<span class="signature">(callback)</span></h3><div class="description"><p>Set a callback function for an event where a user drags a box around multiple atoms. The function should take as arguments a ModelView including the atoms in the box:</p><p>function callback(view) { ... }</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>callback</code></td><td class="type"><span class="param-type">function</span></td><td class="default">null</td><td class="description last"><p>Callback function for the event. Passing &quot;null&quot; restores default behaviour</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line249">line 249</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="onAtomClick"><span class="type-signature"></span>onAtomClick<span class="signature">(callback, modifiers)</span></h3><div class="description"><p>Set a callback function for an event where a user clicks on an atom. The function should take as arguments the atom image for the clicked atom and the event object:</p><p>function callback(atom, event) { ... }</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>callback</code></td><td class="type"><span class="param-type">function</span></td><td class="default">null</td><td class="description last"><p>Callback function for the event. Passing &quot;null&quot; restores default behaviour</p></td></tr><tr><td class="name"><code>modifiers</code></td><td class="type"><span class="param-type">int</span></td><td class="default"></td><td class="description last"><p>Click event. Use the following flags to define it:</p><ul><li>CrystVis.LEFT_CLICK</li><li>CrystVis.RIGHT_CLICK</li><li>CrystVis.MIDDLE_CLICK</li><li>CrystVis.CTRL_BUTTON</li><li>CrystVis.ALT_BUTTON</li><li>CrystVis.SHIFT_BUTTON</li><li>CrystVis.CMD_BUTTON</li></ul><p>For example, CrystVis.LEFT_CLICK + CrystVis.SHIFT_BUTTON defines the event for a click while the Shift key is pressed.</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line219">line 219</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="reloadModel"><span class="type-signature"></span>reloadModel<span class="signature">(name, parameters)</span></h3><div class="description"><p>Reload a model, possibly with new parameters</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="description last"><p>Name of the model to reload.</p></td></tr><tr><td class="name"><code>parameters</code></td><td class="type"><span class="param-type">Object</span></td><td class="description last"><p>Loading parameters as in .loadModels()</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line394">line 394</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="removePrimitive"><span class="type-signature"></span>removePrimitive<span class="signature">(p)</span></h3><div class="description"><p>Remove a primitive shape from the drawing</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>p</code></td><td class="type"><span class="param-type">THREE.<wbr>Object3D</span></td><td class="description last"><p>Primitive to remove</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line501">line 501</a></li></ul></dd></div></dl></article></section></div></div></div><div class="search-container" id="PkfLWpAbet" style="display:none"><div class="wrapper" id="iCxFxjkHbP"><button class="icon-button search-close-button" id="VjLlGakifb" aria-label="close search"><svg><use xlink:href="#close-icon"></use></svg></button><div class="search-box-c"><svg><use xlink:href="#search-icon"></use></svg> <input 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href="lib_model.module_js-AtomImage.html">AtomImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-BondImage.html">BondImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-Model.html">Model</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js-ModelView.html">ModelView</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js-CrystVis.html">CrystVis</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-tutorials"><div>Tutorials</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="tutorial-Events.html">Events</a></div><div class="sidebar-section-children"><a href="tutorial-Queries.html">Queries</a></div><div class="sidebar-section-children"><a href="tutorial-ThreejsMigration.html">ThreejsMigration</a></div></div></div></div></div><div class="navbar-container" id="VuAckcnZhf"><nav class="navbar"><div class="navbar-left-items"></div><div class="navbar-right-items"><div class="navbar-right-item"><button class="icon-button search-button" aria-label="open-search"><svg><use xlink:href="#search-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button theme-toggle" aria-label="toggle-theme"><svg><use class="theme-svg-use" xlink:href="#light-theme-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button font-size" aria-label="change-font-size"><svg><use xlink:href="#font-size-icon"></use></svg></button></div></div><nav></nav></nav></div><div class="toc-container"><div class="toc-content"><span class="bold">On this page</span><div id="eed4d2a0bfd64539bb9df78095dec881"></div></div></div><div class="body-wrapper"><div class="main-content"><div class="main-wrapper"><section><header><h1 id="CrystVis-title" class="has-anchor"><span class="ancestors"><a href="lib_visualizer.module_js.html">lib/visualizer.js</a>~</span> CrystVis</h1><div class="class-description"><p>An object providing a full interface to a renderer for crystallographic models</p></div></header><article><div class="container-overview"><h2 id="constructor" class="has-anchor">Constructor</h2><h3 class="name has-anchor" id="CrystVis"><span class="type-signature"></span>new CrystVis<span class="signature">(element, width, height, rendererOptions)</span></h3><div class="description"><p>An object providing a full interface to a renderer for crystallographic models</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>element</code></td><td class="type"><span class="param-type">string</span></td><td class="default"></td><td class="description last"><p>CSS-style identifier for the HTML element to put the renderer in</p></td></tr><tr><td class="name"><code>width</code></td><td class="type"><span class="param-type">int</span></td><td class="default">0</td><td class="description last"><p>Window width</p></td></tr><tr><td class="name"><code>height</code></td><td class="type"><span class="param-type">int</span></td><td class="default">0</td><td class="description last"><p>Window height. If both this and width are set to 0, the window fits its context and automatically resizes with it</p></td></tr><tr><td class="name"><code>rendererOptions</code></td><td class="type"><span class="param-type">Object</span></td><td class="default"></td><td class="description last"><p>Options for the renderer</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line38">line 38</a></li></ul></dd></div></dl></div><h2 id="members" class="subsection-title has-anchor">Members</h2><h3 class="name has-anchor" id="displayed"><span class="type-signature"></span>displayed<span class="type-signature"> :ModelView</span></h3><div class="description"><p>Displayed atoms</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">ModelView</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line149">line 149</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="highlightSelected"><span class="type-signature"></span>highlightSelected<span class="type-signature"> :bool</span></h3><div class="description"><p>Whether the selected atoms should be highlighted with auras</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">bool</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line182">line 182</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="isDisposed"><span class="type-signature">(readonly) </span>isDisposed<span class="type-signature"> :boolean</span></h3><div class="description"><p>Whether this instance has been disposed. Once true, most methods will throw rather than silently fail.</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">boolean</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line114">line 114</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="model"><span class="type-signature">(readonly) </span>model<span class="type-signature"> :Model</span></h3><div class="description"><p>Currently loaded model</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Model</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line132">line 132</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="modelList"><span class="type-signature">(readonly) </span>modelList<span class="type-signature"> :Array</span></h3><div class="description"><p>List of loaded models</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line123">line 123</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="modelName"><span class="type-signature">(readonly) </span>modelName<span class="type-signature"> :String</span></h3><div class="description"><p>Name of the currently loaded model</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">String</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line141">line 141</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="selected"><span class="type-signature"></span>selected<span class="type-signature"> :ModelView</span></h3><div class="description"><p>Selected atoms</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">ModelView</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line166">line 166</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="theme"><span class="type-signature"></span>theme<span class="type-signature"> :object</span></h3><div class="description"><p>Theme</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">object</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line205">line 205</a></li></ul></dd></div></dl><h2 id="methods" class="subsection-title has-anchor">Methods</h2><h3 class="name has-anchor" id="addNotification"><span class="type-signature"></span>addNotification<span class="signature">()</span></h3><div class="description"><p>Add a notification to the list of notifications to be displayed</p></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line744">line 744</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="addNotifications"><span class="type-signature"></span>addNotifications<span class="signature">()</span></h3><div class="description"><p>Adds all notifications to the drawing</p></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line753">line 753</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="addPrimitive"><span class="type-signature"></span>addPrimitive<span class="signature">(p)</span></h3><div class="description"><p>Add a primitive shape to the drawing</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>p</code></td><td class="type"><span class="param-type">THREE.<wbr>Object3D</span></td><td class="description last"><p>Primitive to add</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line728">line 728</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="clearNotifications"><span class="type-signature"></span>clearNotifications<span class="signature">()</span></h3><div class="description"><p>Removes notifications from the drawing</p></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line764">line 764</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="deleteModel"><span class="type-signature"></span>deleteModel<span class="signature">(name)</span></h3><div class="description"><p>Erase a model from the recorded ones</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="description last"><p>Name of the model to delete</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line706">line 706</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="displayModel"><span class="type-signature"></span>displayModel<span class="signature">(name)</span></h3><div class="description"><p>Render a model</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="default">null</td><td class="description last"><p>Name of the model to display. If empty, just clear the renderer window.</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line651">line 651</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="dispose"><span class="type-signature"></span>dispose<span class="signature">()</span></h3><div class="description"><p>Release all resources held by this instance: cancels the animation loop, removes all canvas event listeners, disposes OrbitControls and the THREE.WebGLRenderer, and nulls internal references. After calling this method the instance must not be used again.</p></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line492">line 492</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="getCameraState"><span class="type-signature"></span>getCameraState<span class="signature">()</span><span class="type-signature"> &rarr; {Object}</span></h3><div class="description"><p>Return a plain serialisable snapshot of the current camera state.</p></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line302">line 302</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">Object</span></dd></dl></div><h3 class="name has-anchor" id="getModelMeta"><span class="type-signature"></span>getModelMeta<span class="signature">(name)</span><span class="type-signature"> &rarr; {Object|null}</span></h3><div class="description"><p>Return metadata stored alongside the named model: <code>{ prefix, originalName }</code>.</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="description last"><p>Model name</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line393">line 393</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">Object</span> |<wbr> <span class="param-type">null</span></dd></dl></div><h3 class="name has-anchor" id="getModelParameters"><span class="type-signature"></span>getModelParameters<span class="signature">(name)</span><span class="type-signature"> &rarr; {Object|null}</span></h3><div class="description"><p>Return the loading parameters that were used when the named model was last loaded / reloaded (a clone of the merged parameter object).</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="description last"><p>Model name</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line381">line 381</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">Object</span> |<wbr> <span class="param-type">null</span></dd></dl></div><h3 class="name has-anchor" id="getModelSource"><span class="type-signature"></span>getModelSource<span class="signature">(name)</span><span class="type-signature"> &rarr; {Object|null}</span></h3><div class="description"><p>Return the raw file text and format extension originally passed to <code>loadModels()</code> for the named model.</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="description last"><p>Model name</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line369">line 369</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">Object</span> |<wbr> <span class="param-type">null</span></dd></dl></div><h3 class="name has-anchor" id="getScreenshotData"><span class="type-signature"></span>getScreenshotData<span class="signature">()</span><span class="type-signature"> &rarr; {String}</span></h3><div class="description"><p>Recover a data URL of a PNG screenshot of the current scene</p></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line774">line 774</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>A data URL of the PNG screenshot</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">String</span></dd></dl></div><h3 class="name has-anchor" id="loadModels"><span class="type-signature"></span>loadModels<span class="signature">(contents, format, prefix, parameters)</span><span class="type-signature"> &rarr; {Object}</span></h3><div class="description"><p>Load one or more atomic models from a file's contents</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>contents</code></td><td class="type"><span class="param-type">String</span></td><td class="default"></td><td class="description last"><p>The contents of the structure file</p></td></tr><tr><td class="name"><code>format</code></td><td class="type"><span class="param-type">String</span></td><td class="default">cif</td><td class="description last"><p>The file's format (cif, xyz, etc.). Default is cif.</p></td></tr><tr><td class="name"><code>prefix</code></td><td class="type"><span class="param-type">String</span></td><td class="default">null</td><td class="description last"><p>Prefix to use when naming the models. Default is empty.</p></td></tr><tr><td class="name"><code>parameters</code></td><td class="type"><span class="param-type">Object</span></td><td class="default"></td><td class="description last"><p>Loading parameters:</p><ul><li><code>supercell</code>: supercell size (only used if the structure is periodic)</li><li><code>molecularCrystal</code>: if true, try to make the model load completing molecules across periodic boundaries</li><li><code>useNMRActiveIsotopes</code>: if true, all isotopes are set by default to the most common one with non-zero spin</li><li><code>vdwScaling</code>: scale van der Waals radii by a constant factor</li><li><code>vdwElementScaling</code>: table of per-element factors to scale VdW radii by</li></ul></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line557">line 557</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Status map of the models we tried to load. Keys are the model names (strings that can be passed directly to <code>displayModel()</code>). Values are <code>0</code> for a successful load, or an error message string if loading failed. Example: to display the first loaded model, use <code>visualizer.displayModel(Object.keys(loaded)[0])</code> and check <code>loaded[modelName] !== 0</code> to detect errors.</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">Object</span></dd></dl></div><h3 class="name has-anchor" id="onAtomBox"><span class="type-signature"></span>onAtomBox<span class="signature">(callback)</span></h3><div class="description"><p>Set a callback function for an event where a user drags a box around multiple atoms. The function should take as arguments a ModelView including the atoms in the box:</p><p>function callback(view) { ... }</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>callback</code></td><td class="type"><span class="param-type">function</span></td><td class="default">null</td><td class="description last"><p>Callback function for the event. Passing &quot;null&quot; restores default behaviour</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line277">line 277</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="onAtomClick"><span class="type-signature"></span>onAtomClick<span class="signature">(callback, modifiers)</span></h3><div class="description"><p>Set a callback function for an event where a user clicks on an atom. The function should take as arguments the atom image for the clicked atom and the event object:</p><p>function callback(atom, event) { ... }</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>callback</code></td><td class="type"><span class="param-type">function</span></td><td class="default">null</td><td class="description last"><p>Callback function for the event. Passing &quot;null&quot; restores default behaviour</p></td></tr><tr><td class="name"><code>modifiers</code></td><td class="type"><span class="param-type">int</span></td><td class="default"></td><td class="description last"><p>Click event. Use the following flags to define it:</p><ul><li>CrystVis.LEFT_CLICK</li><li>CrystVis.RIGHT_CLICK</li><li>CrystVis.MIDDLE_CLICK</li><li>CrystVis.CTRL_BUTTON</li><li>CrystVis.ALT_BUTTON</li><li>CrystVis.SHIFT_BUTTON</li><li>CrystVis.CMD_BUTTON</li></ul><p>For example, CrystVis.LEFT_CLICK + CrystVis.SHIFT_BUTTON defines the event for a click while the Shift key is pressed.</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line247">line 247</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="onCameraChange"><span class="type-signature"></span>onCameraChange<span class="signature">(callback)</span><span class="type-signature"> &rarr; {function}</span></h3><div class="description"><p>Subscribe to camera-change events (rotate, pan, zoom). The callback receives a snapshot identical to CrystVis#getCameraState.</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>callback</code></td><td class="type"><span class="param-type">function</span></td><td class="description last"><p><code>callback(cameraState)</code></p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line323">line 323</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Unsubscribe function</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">function</span></dd></dl></div><h3 class="name has-anchor" id="onDisplayChange"><span class="type-signature"></span>onDisplayChange<span class="signature">(callback)</span><span class="type-signature"> &rarr; {function}</span></h3><div class="description"><p>Subscribe to display-change events fired whenever <code>displayModel()</code> completes. The callback receives the name of the newly displayed model (or <code>null</code> when cleared).</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>callback</code></td><td class="type"><span class="param-type">function</span></td><td class="description last"><p><code>callback(modelName: string|null)</code></p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line353">line 353</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Unsubscribe function</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">function</span></dd></dl></div><h3 class="name has-anchor" id="onModelListChange"><span class="type-signature"></span>onModelListChange<span class="signature">(callback)</span><span class="type-signature"> &rarr; {function}</span></h3><div class="description"><p>Subscribe to model-list change events (model added or deleted). The callback receives the new list of model names.</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>callback</code></td><td class="type"><span class="param-type">function</span></td><td class="description last"><p><code>callback(modelNames: string[])</code></p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line339">line 339</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Unsubscribe function</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">function</span></dd></dl></div><h3 class="name has-anchor" id="reloadModel"><span class="type-signature"></span>reloadModel<span class="signature">(name, parameters)</span></h3><div class="description"><p>Reload a model, possibly with new parameters</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="description last"><p>Name of the model to reload.</p></td></tr><tr><td class="name"><code>parameters</code></td><td class="type"><span class="param-type">Object</span></td><td class="description last"><p>Loading parameters as in .loadModels()</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line617">line 617</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="removePrimitive"><span class="type-signature"></span>removePrimitive<span class="signature">(p)</span></h3><div class="description"><p>Remove a primitive shape from the drawing</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>p</code></td><td class="type"><span class="param-type">THREE.<wbr>Object3D</span></td><td class="description last"><p>Primitive to remove</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line737">line 737</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="setCameraState"><span class="type-signature"></span>setCameraState<span class="signature">(state)</span></h3><div class="description"><p>Restore a camera snapshot produced by CrystVis#getCameraState. Safe to call after <code>displayModel()</code>.</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>state</code></td><td class="type"></td><td class="description last"></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line312">line 312</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="unloadAll"><span class="type-signature"></span>unloadAll<span class="signature">()</span></h3><div class="description"><p>Remove <em>all</em> loaded models and reset the view in a single atomic operation (only one render pass after everything is cleared, unlike calling <code>deleteModel()</code> in a loop).</p></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line405">line 405</a></li></ul></dd></div></dl></article></section></div></div></div><div class="search-container" id="PkfLWpAbet" style="display:none"><div class="wrapper" id="iCxFxjkHbP"><button class="icon-button search-close-button" id="VjLlGakifb" aria-label="close search"><svg><use xlink:href="#close-icon"></use></svg></button><div class="search-box-c"><svg><use xlink:href="#search-icon"></use></svg> <input type="text" id="vpcKVYIppa" class="search-input" placeholder="Search..." autofocus></div><div class="search-result-c" id="fWwVHRuDuN"><span class="search-result-c-text">Type anything to view search result</span></div></div></div><div class="mobile-menu-icon-container"><button class="icon-button" id="mobile-menu" data-isopen="false" aria-label="menu"><svg><use xlink:href="#menu-icon"></use></svg></button></div><div id="mobile-sidebar" class="mobile-sidebar-container"><div class="mobile-sidebar-wrapper"><div class="mobile-nav-links"></div><div class="mobile-sidebar-items-c"><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-modules"><div>Modules</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="lib_model.module_js.html">lib/model.js</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js.html">lib/modelview.js</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js.html">lib/visualizer.js</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-classes"><div>Classes</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="lib_model.module_js-AtomImage.html">AtomImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-BondImage.html">BondImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-Model.html">Model</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js-ModelView.html">ModelView</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js-CrystVis.html">CrystVis</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-tutorials"><div>Tutorials</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="tutorial-Events.html">Events</a></div><div class="sidebar-section-children"><a href="tutorial-Queries.html">Queries</a></div><div class="sidebar-section-children"><a href="tutorial-ThreejsMigration.html">ThreejsMigration</a></div></div></div><div class="mobile-navbar-actions"><div class="navbar-right-item"><button class="icon-button search-button" aria-label="open-search"><svg><use xlink:href="#search-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button theme-toggle" aria-label="toggle-theme"><svg><use class="theme-svg-use" xlink:href="#light-theme-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button font-size" aria-label="change-font-size"><svg><use xlink:href="#font-size-icon"></use></svg></button></div></div></div></div><script type="text/javascript" src="scripts/core.min.js"></script><script src="scripts/search.min.js" defer="defer"></script><script src="scripts/third-party/fuse.js" defer="defer"></script><script type="text/javascript">var tocbotInstance=tocbot.init({tocSelector:"#eed4d2a0bfd64539bb9df78095dec881",contentSelector:".main-content",headingSelector:"h1, h2, h3",hasInnerContainers:!0,scrollContainer:".main-content",headingsOffset:130,onClick:bringLinkToView})</script></body></html>
package/docs/model.js.html CHANGED
@@ -629,9 +629,6 @@ class AtomImage {
629
629
  let seed = utils.hashCode(this._fxyz + name);
630
630
  parameters.ditherSeed = seed/4294967295.0; // Reduce to ]0.5,-0.5]
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631
  }
632
- else {
633
-
634
- }
635
632
 
636
633
  var r = this.renderer;
637
634
  if (r) {
@@ -1781,6 +1778,37 @@ class Model {
1781
1778
  return new ModelView(this, indices);
1782
1779
  }
1783
1780
 
1781
+ /**
1782
+ * Reconstruct a {@link ModelView} from a plain array of atom-image indices,
1783
+ * as produced by {@link ModelView#toIndices}. This is the stable public API
1784
+ * for deserialising a saved selection.
1785
+ *
1786
+ * @param {number[]} indices
1787
+ * @return {ModelView}
1788
+ */
1789
+ viewFromIndices(indices = []) {
1790
+ return this.view(indices);
1791
+ }
1792
+
1793
+ /**
1794
+ * Reconstruct a {@link ModelView} from an array of crystallographic site
1795
+ * labels (`crystLabel`), as produced by {@link ModelView#toLabels}. This
1796
+ * is resilient to atom-index reordering across reloads.
1797
+ *
1798
+ * @param {string[]} labels
1799
+ * @return {ModelView}
1800
+ */
1801
+ viewFromLabels(labels = []) {
1802
+ const wanted = new Set(labels);
1803
+ const indices = [];
1804
+ for (let i = 0; i &lt; this._atom_images.length; ++i) {
1805
+ if (wanted.has(this._atom_images[i].crystLabel)) {
1806
+ indices.push(i);
1807
+ }
1808
+ }
1809
+ return this.view(indices);
1810
+ }
1811
+
1784
1812
  /**
1785
1813
  * Set a property on a series of atom images
1786
1814
  *
package/docs/modelview.js.html CHANGED
@@ -442,6 +442,30 @@ class ModelView {
442
442
  return this;
443
443
  }
444
444
 
445
+ // ─── Serialisation helpers ───────────────────────────────────────────────────
446
+
447
+ /**
448
+ * Return a plain array of the atom-image indices in this view.
449
+ * Use this to serialise a selection; restore it with
450
+ * {@link Model#viewFromIndices}.
451
+ *
452
+ * @return {number[]}
453
+ */
454
+ toIndices() {
455
+ return Array.from(this._indices);
456
+ }
457
+
458
+ /**
459
+ * Return the crystallographic site labels (`crystLabel`) of the atoms
460
+ * in this view. Use this to serialise a selection in a way that is
461
+ * robust to atom reordering; restore with {@link Model#viewFromLabels}.
462
+ *
463
+ * @return {string[]}
464
+ */
465
+ toLabels() {
466
+ return this._images.map(a => a.crystLabel);
467
+ }
468
+
445
469
  }
446
470
 
447
471
  export {