@ccp-nc/crystvis-js 0.7.0 → 0.7.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (44) hide show
  1. package/lib/render.js +41 -15
  2. package/package.json +3 -2
  3. package/test/render.js +168 -0
  4. package/test/setup-dom.cjs +65 -3
  5. package/docs/data/search.json +0 -1
  6. package/docs/fonts/Inconsolata-Regular.ttf +0 -0
  7. package/docs/fonts/OpenSans-Regular.ttf +0 -0
  8. package/docs/fonts/WorkSans-Bold.ttf +0 -0
  9. package/docs/index.html +0 -59
  10. package/docs/lib_model.module_js-AtomImage.html +0 -3
  11. package/docs/lib_model.module_js-BondImage.html +0 -3
  12. package/docs/lib_model.module_js-Model.html +0 -3
  13. package/docs/lib_model.module_js.html +0 -3
  14. package/docs/lib_modelview.module_js-ModelView.html +0 -12
  15. package/docs/lib_modelview.module_js.html +0 -3
  16. package/docs/lib_visualizer.module_js-CrystVis.html +0 -3
  17. package/docs/lib_visualizer.module_js.html +0 -3
  18. package/docs/model.js.html +0 -2191
  19. package/docs/modelview.js.html +0 -473
  20. package/docs/scripts/core.js +0 -726
  21. package/docs/scripts/core.min.js +0 -23
  22. package/docs/scripts/resize.js +0 -90
  23. package/docs/scripts/search.js +0 -265
  24. package/docs/scripts/search.min.js +0 -6
  25. package/docs/scripts/third-party/Apache-License-2.0.txt +0 -202
  26. package/docs/scripts/third-party/fuse.js +0 -9
  27. package/docs/scripts/third-party/hljs-line-num-original.js +0 -369
  28. package/docs/scripts/third-party/hljs-line-num.js +0 -1
  29. package/docs/scripts/third-party/hljs-original.js +0 -5171
  30. package/docs/scripts/third-party/hljs.js +0 -1
  31. package/docs/scripts/third-party/popper.js +0 -5
  32. package/docs/scripts/third-party/tippy.js +0 -1
  33. package/docs/scripts/third-party/tocbot.js +0 -672
  34. package/docs/scripts/third-party/tocbot.min.js +0 -1
  35. package/docs/styles/clean-jsdoc-theme-base.css +0 -1159
  36. package/docs/styles/clean-jsdoc-theme-dark.css +0 -412
  37. package/docs/styles/clean-jsdoc-theme-light.css +0 -482
  38. package/docs/styles/clean-jsdoc-theme-scrollbar.css +0 -30
  39. package/docs/styles/clean-jsdoc-theme-without-scrollbar.min.css +0 -1
  40. package/docs/styles/clean-jsdoc-theme.min.css +0 -1
  41. package/docs/tutorial-Events.html +0 -13
  42. package/docs/tutorial-Queries.html +0 -16
  43. package/docs/tutorial-ThreejsMigration.html +0 -25
  44. package/docs/visualizer.js.html +0 -810
package/docs/lib_model.module_js-AtomImage.html DELETED
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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="AtomImage-title" class="has-anchor"><span class="ancestors"><a href="lib_model.module_js.html">lib/model.js</a>~</span> AtomImage</h1><div class="class-description"><p>An 'image' of a single atom from a model. This represents a specific periodic copy of that atom (if applicable).</p></div></header><article><div class="container-overview"><h2 id="constructor" class="has-anchor">Constructor</h2><h3 class="name has-anchor" id="AtomImage"><span class="type-signature"></span>new AtomImage<span class="signature">(model, index, ijk)</span></h3><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>model</code></td><td class="type"><span class="param-type">Model</span></td><td class="description last"><p>The model from which the image is from</p></td></tr><tr><td class="name"><code>index</code></td><td class="type"><span class="param-type">int</span></td><td class="description last"><p>Index of the atom in the model</p></td></tr><tr><td class="name"><code>ijk</code></td><td class="type"><span class="param-type">Array</span></td><td class="description last"><p>Indices of the cell in which the image is located</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="model.js.html">model.js</a>, <a href="model.js.html#line32">line 32</a></li></ul></dd></div></dl></div><h2 id="members" class="subsection-title has-anchor">Members</h2><h3 class="name has-anchor" id="aura"><span class="type-signature">(readonly) </span>aura<span class="type-signature"> :AuraMesh</span></h3><div class="description"><p>Aura used to highlight this atom image</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">AuraMesh</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="model.js.html">model.js</a>, <a href="model.js.html#line364">line 364</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="baseRadius"><span class="type-signature"></span>baseRadius<span class="type-signature"> :float</span></h3><div class="description"><p>Starting radius of the atom</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">float</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="model.js.html">model.js</a>, <a href="model.js.html#line418">line 418</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="bondedAtoms"><span class="type-signature">(readonly) </span>bondedAtoms<span class="type-signature"> :Array.&lt;AtomImage></span></h3><div class="description"><p>All atoms bonded to this atom</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;AtomImage></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="model.js.html">model.js</a>, <a href="model.js.html#line282">line 282</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="bonds"><span class="type-signature">(readonly) </span>bonds<span class="type-signature"> :Array.&lt;BondImage></span></h3><div class="description"><p>All bonds connected to this atom</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;BondImage></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="model.js.html">model.js</a>, <a href="model.js.html#line273">line 273</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="bondsFrom"><span class="type-signature">(readonly) </span>bondsFrom<span class="type-signature"> :Array.&lt;BondImage></span></h3><div class="description"><p>Bonds from this atom</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;BondImage></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="model.js.html">model.js</a>, <a href="model.js.html#line255">line 255</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="bondsTo"><span class="type-signature">(readonly) </span>bondsTo<span class="type-signature"> :Array.&lt;BondImage></span></h3><div class="description"><p>Bonds to this atom</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;BondImage></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="model.js.html">model.js</a>, <a href="model.js.html#line264">line 264</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="color"><span class="type-signature"></span>color<span class="type-signature"> :int</span></h3><div class="description"><p>Color of the atom</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">int</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="model.js.html">model.js</a>, <a href="model.js.html#line467">line 467</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="cpkColor"><span class="type-signature">(readonly) </span>cpkColor<span class="type-signature"> :int</span></h3><div class="description"><p>Hex integer code of the conventional CPK color used for this element (altered in case of non-standard isotopes)</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">int</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="model.js.html">model.js</a>, <a href="model.js.html#line237">line 237</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="crystLabel"><span class="type-signature">(readonly) </span>crystLabel<span class="type-signature"> :String</span></h3><div class="description"><p>Crystal site label of this atom</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="model.js.html">model.js</a>, <a href="model.js.html#line162">line 162</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="element"><span class="type-signature">(readonly) </span>element<span class="type-signature"> :String</span></h3><div class="description"><p>Symbol of this atom's element</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="model.js.html">model.js</a>, <a href="model.js.html#line153">line 153</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="elementData"><span class="type-signature">(readonly) </span>elementData<span class="type-signature"> :Object</span></h3><div class="description"><p>Periodic table information for this atom's element</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="model.js.html">model.js</a>, <a href="model.js.html#line171">line 171</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="fxyz"><span class="type-signature">(readonly) </span>fxyz<span class="type-signature"> :Array.&lt;float></span></h3><div class="description"><p>Fractional coordinates of this atom image</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;float></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="model.js.html">model.js</a>, <a href="model.js.html#line332">line 332</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="fxyz0"><span class="type-signature">(readonly) </span>fxyz0<span class="type-signature"> :Array.&lt;float></span></h3><div class="description"><p>Fractional coordinates of this atom's original</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;float></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="model.js.html">model.js</a>, <a href="model.js.html#line323">line 323</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="highlighted"><span class="type-signature"></span>highlighted<span class="type-signature"> :bool</span></h3><div class="description"><p>Whether the atom is highlighted</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="model.js.html">model.js</a>, <a href="model.js.html#line524">line 524</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="id"><span class="type-signature">(readonly) </span>id<span class="type-signature"> :String</span></h3><div class="description"><p>String ID of the image</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="model.js.html">model.js</a>, <a href="model.js.html#line126">line 126</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="ijk"><span class="type-signature">(readonly) </span>ijk<span class="type-signature"> :Array.&lt;int></span></h3><div class="description"><p>Cell indices of this atom image</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;int></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="model.js.html">model.js</a>, <a href="model.js.html#line296">line 296</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="imgIndex"><span class="type-signature">(readonly) </span>imgIndex<span class="type-signature"> :int</span></h3><div class="description"><p>Index of this image</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">int</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="model.js.html">model.js</a>, <a href="model.js.html#line135">line 135</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="index"><span class="type-signature">(readonly) </span>index<span class="type-signature"> :int</span></h3><div class="description"><p>Index of the atom</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">int</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="model.js.html">model.js</a>, <a href="model.js.html#line117">line 117</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="isotope"><span class="type-signature"></span>isotope<span class="type-signature"> :int</span></h3><div class="description"><p>Atomic mass of this atom's isotope</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">int</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="model.js.html">model.js</a>, <a href="model.js.html#line191">line 191</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="isotopeData"><span class="type-signature">(readonly) </span>isotopeData<span class="type-signature"> :Object</span></h3><div class="description"><p>Information for this atom's isotope</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="model.js.html">model.js</a>, <a href="model.js.html#line180">line 180</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="isotopeGlobal"><span class="type-signature"></span>isotopeGlobal<span class="type-signature"> :int</span></h3><div class="description"><p>Atomic mass of the global isotope set as default for this atom's species</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">int</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="model.js.html">model.js</a>, <a href="model.js.html#line209">line 209</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="mesh"><span class="type-signature">(readonly) </span>mesh<span class="type-signature"> :AtomMesh</span></h3><div class="description"><p>Mesh corresponding to this atom image</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">AtomMesh</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="model.js.html">model.js</a>, <a href="model.js.html#line350">line 350</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>Model this atom belongs to</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="model.js.html">model.js</a>, <a href="model.js.html#line93">line 93</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="moleculeIndex"><span class="type-signature">(readonly) </span>moleculeIndex<span class="type-signature"> :int</span></h3><div class="description"><p>Index of the molecule this atom belongs to</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">int</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="model.js.html">model.js</a>, <a href="model.js.html#line341">line 341</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="number"><span class="type-signature">(readonly) </span>number<span class="type-signature"> :int</span></h3><div class="description"><p>Atomic number of element</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">int</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="model.js.html">model.js</a>, <a href="model.js.html#line226">line 226</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="opacity"><span class="type-signature"></span>opacity<span class="type-signature"> :float</span></h3><div class="description"><p>Opacity of the atom</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">float</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="model.js.html">model.js</a>, <a href="model.js.html#line499">line 499</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="radius"><span class="type-signature"></span>radius<span class="type-signature"> :float</span></h3><div class="description"><p>Final radius of the atom (starting radius * scale)</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">float</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="model.js.html">model.js</a>, <a href="model.js.html#line452">line 452</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="renderer"><span class="type-signature">(readonly) </span>renderer<span class="type-signature"> :Renderer</span></h3><div class="description"><p>Renderer used by this atom</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Renderer</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="model.js.html">model.js</a>, <a href="model.js.html#line102">line 102</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="scale"><span class="type-signature"></span>scale<span class="type-signature"> :float</span></h3><div class="description"><p>Scale of the atom</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">float</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="model.js.html">model.js</a>, <a href="model.js.html#line435">line 435</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="speciesIndex"><span class="type-signature">(readonly) </span>speciesIndex<span class="type-signature"> :int</span></h3><div class="description"><p>Index of the species of this atom</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">int</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="model.js.html">model.js</a>, <a href="model.js.html#line144">line 144</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="vdwRadius"><span class="type-signature">(readonly) </span>vdwRadius<span class="type-signature"> :float</span></h3><div class="description"><p>Van dew Waals radius for this element</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">float</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="model.js.html">model.js</a>, <a href="model.js.html#line246">line 246</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="visible"><span class="type-signature"></span>visible<span class="type-signature"> :bool</span></h3><div class="description"><p>Whether the atom is visible</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="model.js.html">model.js</a>, <a href="model.js.html#line383">line 383</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="xyz"><span class="type-signature">(readonly) </span>xyz<span class="type-signature"> :Array.&lt;float></span></h3><div class="description"><p>Position of this atom image</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;float></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="model.js.html">model.js</a>, <a href="model.js.html#line314">line 314</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="xyz0"><span class="type-signature">(readonly) </span>xyz0<span class="type-signature"> :Array.&lt;float></span></h3><div class="description"><p>Position of this atom's original</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;float></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="model.js.html">model.js</a>, <a href="model.js.html#line305">line 305</a></li></ul></dd></div></dl><h2 id="methods" class="subsection-title has-anchor">Methods</h2><h3 class="name has-anchor" id="addEllipsoid"><span class="type-signature"></span>addEllipsoid<span class="signature">(data, name, parameters)</span></h3><div class="description"><p>Add an ellipsoid to the atom.</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>data</code></td><td class="type"><span class="param-type">TensorData</span> |<wbr> <span class="param-type">Object</span> |<wbr> <span class="param-type">Array</span></td><td class="description last"><p>The data to base the ellipsoid on. Can be: - a TensorData object; - an Object with 'eigenvalues' and 'eigenvectors' members - an Array of the form [eigenvalues, eigenvectors]</p></td></tr><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 ellipsoid</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>Additional options to pass (see EllipsoidMesh)</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="model.js.html">model.js</a>, <a href="model.js.html#line612">line 612</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="addLabel"><span class="type-signature"></span>addLabel<span class="signature">(text, name, parameters)</span></h3><div class="description"><p>Add a text label to the atom.</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>text</code></td><td class="type"><span class="param-type">String</span></td><td class="description last"><p>Content of the label</p></td></tr><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="description last"><p>Name to use to refer to the label (necessary to overwrite/erase later)</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>Dictionary of other options (e.g. font family, text color, etc. See TextSprite)</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="model.js.html">model.js</a>, <a href="model.js.html#line548">line 548</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="ellipsoidProperty"><span class="type-signature"></span>ellipsoidProperty<span class="signature">(name, property, value)</span></h3><div class="description"><p>Retrieve or set an ellipsoid's properties</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"></td><td class="description last"><p>Name of the ellipsoid</p></td></tr><tr><td class="name"><code>property</code></td><td class="type"><span class="param-type">String</span></td><td class="default"></td><td class="description last"><p>Property to set</p></td></tr><tr><td class="name"><code>value</code></td><td class="type"><span class="param-type">?</span></td><td class="default">null</td><td class="description last"><p>Value to set. If omitted, returns the current value instead.</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="model.js.html">model.js</a>, <a href="model.js.html#line659">line 659</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="getArrayValue"><span class="type-signature"></span>getArrayValue<span class="signature">(name)</span><span class="type-signature"> &rarr; {*}</span></h3><div class="description"><p>Get the value for one array for this image</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 array</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="model.js.html">model.js</a>, <a href="model.js.html#line673">line 673</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Value of the array for this atom</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">*</span></dd></dl></div><h3 class="name has-anchor" id="labelProperty"><span class="type-signature"></span>labelProperty<span class="signature">(name, property, value)</span></h3><div class="description"><p>Retrieve or set a label's properties</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"></td><td class="description last"><p>Name of the label</p></td></tr><tr><td class="name"><code>property</code></td><td class="type"><span class="param-type">String</span></td><td class="default"></td><td class="description last"><p>Property to set</p></td></tr><tr><td class="name"><code>value</code></td><td class="type"><span class="param-type">?</span></td><td class="default">null</td><td class="description last"><p>Value to set. If omitted, returns the current value instead.</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="model.js.html">model.js</a>, <a href="model.js.html#line590">line 590</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="removeEllipsoid"><span class="type-signature"></span>removeEllipsoid<span class="signature">(name)</span></h3><div class="description"><p>Remove the ellipsoid with a given name</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 ellipsoid</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="model.js.html">model.js</a>, <a href="model.js.html#line644">line 644</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="removeLabel"><span class="type-signature"></span>removeLabel<span class="signature">(name)</span></h3><div class="description"><p>Remove the label of a given name</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 label</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="model.js.html">model.js</a>, <a href="model.js.html#line574">line 574</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 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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="BondImage-title" class="has-anchor"><span class="ancestors"><a href="lib_model.module_js.html">lib/model.js</a>~</span> BondImage</h1><div class="class-description"><p>An 'image' of a single bond in the model. This represents the connection between two specific AtomImages</p></div></header><article><div class="container-overview"><h2 id="constructor" class="has-anchor">Constructor</h2><h3 class="name has-anchor" id="BondImage"><span class="type-signature"></span>new BondImage<span class="signature">(model, im1, im2)</span></h3><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>model</code></td><td class="type"><span class="param-type">Model</span></td><td class="description last"><p>The model from which the image is from</p></td></tr><tr><td class="name"><code>im1</code></td><td class="type"><span class="param-type">AtomImage</span></td><td class="description last"><p>AtomImage from which the bond starts</p></td></tr><tr><td class="name"><code>im2</code></td><td class="type"><span class="param-type">AtomImage</span></td><td class="description last"><p>AtomImage to which the bond ends</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="model.js.html">model.js</a>, <a href="model.js.html#line694">line 694</a></li></ul></dd></div></dl></div><h2 id="members" class="subsection-title has-anchor">Members</h2><h3 class="name has-anchor" id="atom1"><span class="type-signature">(readonly) </span>atom1<span class="type-signature"> :AtomImage</span></h3><div class="description"><p>First atom connected to this bond</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">AtomImage</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="model.js.html">model.js</a>, <a href="model.js.html#line752">line 752</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="atom2"><span class="type-signature">(readonly) </span>atom2<span class="type-signature"> :AtomImage</span></h3><div class="description"><p>Second atom connected to this bond</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">AtomImage</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="model.js.html">model.js</a>, <a href="model.js.html#line761">line 761</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="color1"><span class="type-signature"></span>color1<span class="type-signature"> :int</span></h3><div class="description"><p>First color of the bond</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">int</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="model.js.html">model.js</a>, <a href="model.js.html#line822">line 822</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="color2"><span class="type-signature"></span>color2<span class="type-signature"> :int</span></h3><div class="description"><p>Second color of the bond</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">int</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="model.js.html">model.js</a>, <a href="model.js.html#line836">line 836</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="key"><span class="type-signature">(readonly) </span>key<span class="type-signature"> :String</span></h3><div class="description"><p>A unique string key used to quickly reference the bond</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="model.js.html">model.js</a>, <a href="model.js.html#line770">line 770</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="length"><span class="type-signature">(readonly) </span>length<span class="type-signature"> :float</span></h3><div class="description"><p>Bond length in Angstroms</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">float</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="model.js.html">model.js</a>, <a href="model.js.html#line780">line 780</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="mesh"><span class="type-signature">(readonly) </span>mesh<span class="type-signature"> :AtomMesh</span></h3><div class="description"><p>Mesh corresponding to this bond image</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">AtomMesh</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="model.js.html">model.js</a>, <a href="model.js.html#line789">line 789</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>Model this bond belongs to</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="model.js.html">model.js</a>, <a href="model.js.html#line730">line 730</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="opacity1"><span class="type-signature"></span>opacity1<span class="type-signature"> :float</span></h3><div class="description"><p>First opacity of the bond</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">float</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="model.js.html">model.js</a>, <a href="model.js.html#line850">line 850</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="opacity2"><span class="type-signature"></span>opacity2<span class="type-signature"> :float</span></h3><div class="description"><p>Second opacity of the bond</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">float</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="model.js.html">model.js</a>, <a href="model.js.html#line864">line 864</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="radius"><span class="type-signature"></span>radius<span class="type-signature"> :float</span></h3><div class="description"><p>Radius of the bond</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">float</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="model.js.html">model.js</a>, <a href="model.js.html#line803">line 803</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="renderer"><span class="type-signature">(readonly) </span>renderer<span class="type-signature"> :Renderer</span></h3><div class="description"><p>Renderer used by this bond</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Renderer</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="model.js.html">model.js</a>, <a href="model.js.html#line739">line 739</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="visible"><span class="type-signature"></span>visible<span class="type-signature"> :bool</span></h3><div class="description"><p>Whether the bond is visible</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="model.js.html">model.js</a>, <a href="model.js.html#line878">line 878</a></li></ul></dd></div></dl></article></section></div></div></div><div class="search-container" id="PkfLWpAbet" style="display:none"><div 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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="Model-title" class="has-anchor"><span class="ancestors"><a href="lib_model.module_js.html">lib/model.js</a>~</span> Model</h1></header><article><div class="container-overview"><h3 class="name has-anchor" id="Model"><span class="type-signature"></span>new Model<span class="signature">(atoms, parameters)</span></h3><div class="description"><p>An object containing an Atomic structure and taking care of its periodic nature, allowing querying and selection, and so on.</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>atoms</code></td><td class="type"><span class="param-type">crystcif.<wbr>Atoms</span></td><td class="description last"><p>Atomic structure, in crystcif's Atoms format</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>Additional options:</p><ul><li><code>supercell</code></li><li><code>molecularCrystal</code> (if true, load full molecules in central unit cell)</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="model.js.html">model.js</a>, <a href="model.js.html#line914">line 914</a></li></ul></dd></div></dl></div><h2 id="members" class="subsection-title has-anchor">Members</h2><h3 class="name has-anchor" id="all"><span class="type-signature">(readonly) </span>all<span class="type-signature"> :ModelView</span></h3><div class="description"><p>ModelView containing all the atoms of the image</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="model.js.html">model.js</a>, <a href="model.js.html#line1230">line 1230</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="atoms"><span class="type-signature">(readonly) </span>atoms<span class="type-signature"> :Array.&lt;AtomImage></span></h3><div class="description"><p>Atom images in this model</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;AtomImage></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="model.js.html">model.js</a>, <a href="model.js.html#line1221">line 1221</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="axes"><span class="type-signature">(readonly) </span>axes<span class="type-signature"> :AxesMesh</span></h3><div class="description"><p>Graphical object representing the unit cell's axes</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">AxesMesh</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="model.js.html">model.js</a>, <a href="model.js.html#line1239">line 1239</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="box"><span class="type-signature">(readonly) </span>box<span class="type-signature"> :BoxMesh</span></h3><div class="description"><p>Graphical object representing the unit cell's box</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">BoxMesh</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="model.js.html">model.js</a>, <a href="model.js.html#line1248">line 1248</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="cell"><span class="type-signature">(readonly) </span>cell<span class="type-signature"> :Array.&lt;Array></span></h3><div class="description"><p>Unit cell of the model's original cell</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;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="model.js.html">model.js</a>, <a href="model.js.html#line1149">line 1149</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="crystalLabels"><span class="type-signature">(readonly) </span>crystalLabels<span class="type-signature"> :Array.&lt;String></span></h3><div class="description"><p>Crystallographic labels of each atom</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;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="model.js.html">model.js</a>, <a href="model.js.html#line1194">line 1194</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="info"><span class="type-signature">(readonly) </span>info<span class="type-signature"> :Object</span></h3><div class="description"><p>Additional information from the model's original cell</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="model.js.html">model.js</a>, <a href="model.js.html#line1167">line 1167</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="length"><span class="type-signature">(readonly) </span>length<span class="type-signature"> :int</span></h3><div class="description"><p>Number of atoms in this model's original cell</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">int</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="model.js.html">model.js</a>, <a href="model.js.html#line1104">line 1104</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="numbers"><span class="type-signature">(readonly) </span>numbers<span class="type-signature"> :Array.&lt;int></span></h3><div class="description"><p>Atomic numbers in this model's original cell</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;int></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="model.js.html">model.js</a>, <a href="model.js.html#line1122">line 1122</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="pbc"><span class="type-signature">(readonly) </span>pbc<span class="type-signature"> :Array.&lt;bool></span></h3><div class="description"><p>Periodic boundary conditions</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;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="model.js.html">model.js</a>, <a href="model.js.html#line1158">line 1158</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="periodic"><span class="type-signature">(readonly) </span>periodic<span class="type-signature"> :bool</span></h3><div class="description"><p>Whether this model is periodic in all three directions of space</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="model.js.html">model.js</a>, <a href="model.js.html#line1176">line 1176</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="positions"><span class="type-signature">(readonly) </span>positions<span class="type-signature"> :Array.&lt;Array></span></h3><div class="description"><p>Coordinates of the atoms in this model's original cell</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;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="model.js.html">model.js</a>, <a href="model.js.html#line1131">line 1131</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="renderer"><span class="type-signature"></span>renderer<span class="type-signature"> :Renderer</span></h3><div class="description"><p>Renderer used for this model's graphics</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Renderer</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="model.js.html">model.js</a>, <a href="model.js.html#line1274">line 1274</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="scaledPositions"><span class="type-signature">(readonly) </span>scaledPositions<span class="type-signature"> :Array.&lt;Array></span></h3><div class="description"><p>Fractional coordinates of the atoms in this model's original cell</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;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="model.js.html">model.js</a>, <a href="model.js.html#line1140">line 1140</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="speciesIndices"><span class="type-signature">(readonly) </span>speciesIndices<span class="type-signature"> :Array.&lt;int></span></h3><div class="description"><p>Indices of each atom by their species (e.g. C1, C2, H1, C3, H2, etc.)</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;int></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="model.js.html">model.js</a>, <a href="model.js.html#line1185">line 1185</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="supercell"><span class="type-signature">(readonly) </span>supercell<span class="type-signature"> :Array.&lt;int></span></h3><div class="description"><p>Shape of the supercell for this model</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;int></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="model.js.html">model.js</a>, <a href="model.js.html#line1203">line 1203</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="supercellGrid"><span class="type-signature">(readonly) </span>supercellGrid<span class="type-signature"> :Array.&lt;Array></span></h3><div class="description"><p>Full grid of origin coordinates of the cells making up the supercell</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;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="model.js.html">model.js</a>, <a href="model.js.html#line1212">line 1212</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="symbols"><span class="type-signature">(readonly) </span>symbols<span class="type-signature"> :Array.&lt;String></span></h3><div class="description"><p>Chemical symbols in this model's original cell</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array.&lt;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="model.js.html">model.js</a>, <a href="model.js.html#line1113">line 1113</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="vdwElementScaling"><span class="type-signature">(readonly) </span>vdwElementScaling<span class="type-signature"> :Object</span></h3><div class="description"><p>Table of scaling factors by element for Van der Waals radii</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="model.js.html">model.js</a>, <a href="model.js.html#line1266">line 1266</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="vdwScaling"><span class="type-signature">(readonly) </span>vdwScaling<span class="type-signature"> :float</span></h3><div class="description"><p>Global scaling factor for Van der Waals radii</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">float</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="model.js.html">model.js</a>, <a href="model.js.html#line1257">line 1257</a></li></ul></dd></div></dl><h2 id="methods" class="subsection-title has-anchor">Methods</h2><h3 class="name has-anchor" id="absToFrac"><span class="type-signature"></span>absToFrac<span class="signature">(x)</span><span class="type-signature"> &rarr; {Array.&lt;float>}</span></h3><div class="description"><p>Convert absolute coordinates to fractional</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>x</code></td><td class="type"><span class="param-type">Array.&lt;float></span></td><td class="description last"><p>Absolute coordinates</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="model.js.html">model.js</a>, <a href="model.js.html#line1714">line 1714</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Fractional coordinates</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">Array.&lt;float></span></dd></dl></div><h3 class="name has-anchor" id="addLink"><span class="type-signature"></span>addLink<span class="signature">(from, to, name, label, parameters)</span></h3><div class="description"><p>Add link drawn on 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>from</code></td><td class="type"><span class="param-type">Atom</span> |<wbr> <span class="param-type">Array</span></td><td class="default"></td><td class="description last"><p>Starting point</p></td></tr><tr><td class="name"><code>to</code></td><td class="type"><span class="param-type">Atom</span> |<wbr> <span class="param-type">Array</span></td><td class="default"></td><td class="description last"><p>End point</p></td></tr><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="default">link</td><td class="description last"><p>Name to use for the link object</p></td></tr><tr><td class="name"><code>label</code></td><td class="type"><span class="param-type">String</span></td><td class="default">null</td><td class="description last"><p>Text label to add to the link</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>Additional parameters (see LineMesh)</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="model.js.html">model.js</a>, <a href="model.js.html#line1357">line 1357</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="addSphere"><span class="type-signature"></span>addSphere<span class="signature">(center, radius, name, parameters)</span></h3><div class="description"><p>Add a sphere drawn on 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>center</code></td><td class="type"><span class="param-type">Atom</span> |<wbr> <span class="param-type">Array</span></td><td class="default"></td><td class="description last"><p>Center of the sphere</p></td></tr><tr><td class="name"><code>radius</code></td><td class="type"><span class="param-type">float</span></td><td class="default"></td><td class="description last"><p>Radius of the sphere</p></td></tr><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="default">sphere</td><td class="description last"><p>Name to use for the sphere object</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>Additional parameters (see EllipsoidMesh)</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="model.js.html">model.js</a>, <a href="model.js.html#line1392">line 1392</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="clearGraphics"><span class="type-signature"></span>clearGraphics<span class="signature">()</span></h3><div class="description"><p>Remove all graphical objects</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="model.js.html">model.js</a>, <a href="model.js.html#line1438">line 1438</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="deleteArray"><span class="type-signature"></span>deleteArray<span class="signature">(name)</span></h3><div class="description"><p>Delete an array from the underlying Atoms 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>Name of the array 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="model.js.html">model.js</a>, <a href="model.js.html#line1341">line 1341</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="find"><span class="type-signature"></span>find<span class="signature">(query)</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Find a group of atoms based on a given query and return as AtomImages</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>query</code></td><td class="type"><span class="param-type">Array</span></td><td class="description last"><p>A search query for atoms. Must use nested lists of types and arguments, and can use logic operators $and, $or and $xor.</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="model.js.html">model.js</a>, <a href="model.js.html#line1765">line 1765</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>ModelView object for found atoms</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">ModelView</span></dd></dl></div><h3 class="name has-anchor" id="fracToAbs"><span class="type-signature"></span>fracToAbs<span class="signature">(fx)</span><span class="type-signature"> &rarr; {Array.&lt;float>}</span></h3><div class="description"><p>Convert fractional coordinates to absolute</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>fx</code></td><td class="type"><span class="param-type">Array.&lt;float></span></td><td class="description last"><p>Fractional coordinates</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="model.js.html">model.js</a>, <a href="model.js.html#line1697">line 1697</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Absolute coordinates</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">Array.&lt;float></span></dd></dl></div><h3 class="name has-anchor" id="getArray"><span class="type-signature"></span>getArray<span class="signature">(name)</span><span class="type-signature"> &rarr; {Array}</span></h3><div class="description"><p>Retrieve an array from the underlying Atoms 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>Name of the array to retrieve</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="model.js.html">model.js</a>, <a href="model.js.html#line1324">line 1324</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Retrieved array</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">Array</span></dd></dl></div><h3 class="name has-anchor" id="hasArray"><span class="type-signature"></span>hasArray<span class="signature">(name)</span><span class="type-signature"> &rarr; {bool}</span></h3><div class="description"><p>Check if an array exists in the underlying Atoms 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>Name of the array to check</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="model.js.html">model.js</a>, <a href="model.js.html#line1333">line 1333</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Whether the array exists</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">bool</span></dd></dl></div><h3 class="name has-anchor" id="minimumSupercell"><span class="type-signature"></span>minimumSupercell<span class="signature">(r)</span></h3><div class="description"><p>Compute and return the minimum supercell that guarantees containing all atoms at a maximum distance r from those in the [0,0,0] cell.</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>r</code></td><td class="type"><span class="param-type">float</span></td><td class="description last"><p>Maximum distance that must be contained within the supercell</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="model.js.html">model.js</a>, <a href="model.js.html#line1732">line 1732</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="removeGraphics"><span class="type-signature"></span>removeGraphics<span class="signature">(name)</span></h3><div class="description"><p>Remove the graphical object with a given name</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 graphical object 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="model.js.html">model.js</a>, <a href="model.js.html#line1427">line 1427</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="setArray"><span class="type-signature"></span>setArray<span class="signature">(name, arr)</span></h3><div class="description"><p>Set an array for the underlying Atoms 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>Name of the array to use</p></td></tr><tr><td class="name"><code>arr</code></td><td class="type"><span class="param-type">Array</span></td><td class="description last"><p>Array to store</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="model.js.html">model.js</a>, <a href="model.js.html#line1315">line 1315</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="view"><span class="type-signature"></span>view<span class="signature">(indices)</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Create a new ModelView for this model, using a given list of indices</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>indices</code></td><td class="type"><span class="param-type">Array</span></td><td class="description last"><p>Indices of atoms to include in the ModelView</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="model.js.html">model.js</a>, <a href="model.js.html#line1775">line 1775</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>ModelView object for specified indices</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">ModelView</span></dd></dl></div><h3 class="name has-anchor" id="viewFromIndices"><span class="type-signature"></span>viewFromIndices<span class="signature">(indices)</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Reconstruct a ModelView from a plain array of atom-image indices, as produced by ModelView#toIndices. This is the stable public API for deserialising a saved selection.</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>indices</code></td><td class="type"><span class="param-type">Array.&lt;number></span></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="model.js.html">model.js</a>, <a href="model.js.html#line1787">line 1787</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">ModelView</span></dd></dl></div><h3 class="name has-anchor" id="viewFromLabels"><span class="type-signature"></span>viewFromLabels<span class="signature">(labels)</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Reconstruct a ModelView from an array of crystallographic site labels (<code>crystLabel</code>), as produced by ModelView#toLabels. This is resilient to atom-index reordering across reloads.</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>labels</code></td><td class="type"><span class="param-type">Array.&lt;string></span></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="model.js.html">model.js</a>, <a href="model.js.html#line1799">line 1799</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">ModelView</span></dd></dl></div></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>
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