@ccp-nc/crystvis-js 0.6.1 → 0.7.0

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 (32) hide show
  1. package/.mocharc.yml +4 -0
  2. package/.vscode/settings.json +5 -1
  3. package/CHANGELOG.md +54 -16
  4. package/README.md +75 -2
  5. package/audit.txt +12 -25
  6. package/changes.txt +1 -26
  7. package/demo/demo.css +15 -10
  8. package/demo/index.html +32 -5
  9. package/demo/main.js +149 -42
  10. package/docs/data/search.json +1 -1
  11. package/docs/index.html +51 -2
  12. package/docs/lib_model.module_js-Model.html +1 -1
  13. package/docs/lib_modelview.module_js-ModelView.html +1 -1
  14. package/docs/lib_visualizer.module_js-CrystVis.html +1 -1
  15. package/docs/model.js.html +31 -0
  16. package/docs/modelview.js.html +24 -0
  17. package/docs/visualizer.js.html +237 -1
  18. package/lib/formats/magres.js +156 -1
  19. package/lib/model.js +31 -0
  20. package/lib/modelview.js +24 -0
  21. package/lib/render.js +97 -2
  22. package/lib/selbox.js +18 -4
  23. package/lib/visualizer.js +237 -1
  24. package/outdated.txt +9 -12
  25. package/package.json +5 -4
  26. package/test/data/hf_mu_test.magres +62 -0
  27. package/test/data/hf_test.magres +61 -0
  28. package/test/data/optimized_muon_65-hf.magres +1424 -0
  29. package/test/loader.js +115 -1
  30. package/test/model.js +118 -0
  31. package/test/setup-dom.cjs +147 -0
  32. package/test/visualizer.js +475 -0
package/docs/lib_model.module_js-Model.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="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></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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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>
package/docs/lib_modelview.module_js-ModelView.html CHANGED
@@ -9,4 +9,4 @@
9
9
 
10
10
  If left empty, the property is
11
11
  restored to its default value.
12
- </code></pre></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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line263">line 263</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="show"><span class="type-signature"></span>show<span class="signature">()</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Make all atoms in the view visible. Can be chained</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line112">line 112</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="uniqueSites"><span class="type-signature"></span>uniqueSites<span class="signature">()</span></h3><div class="description"><p>Unique atoms in the current view (based on site labels)</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line215">line 215</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="xor"><span class="type-signature"></span>xor<span class="signature">(mview)</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Exclusive OR with another ModelView</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>mview</code></td><td class="type"><span class="param-type">ModelView</span></td><td class="description last"><p>Other view</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line186">line 186</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Result</p></div><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>
12
+ </code></pre></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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line263">line 263</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="show"><span class="type-signature"></span>show<span class="signature">()</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Make all atoms in the view visible. Can be chained</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line112">line 112</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="toIndices"><span class="type-signature"></span>toIndices<span class="signature">()</span><span class="type-signature"> &rarr; {Array.&lt;number>}</span></h3><div class="description"><p>Return a plain array of the atom-image indices in this view. Use this to serialise a selection; restore it with Model#viewFromIndices.</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line452">line 452</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">Array.&lt;number></span></dd></dl></div><h3 class="name has-anchor" id="toLabels"><span class="type-signature"></span>toLabels<span class="signature">()</span><span class="type-signature"> &rarr; {Array.&lt;string>}</span></h3><div class="description"><p>Return the crystallographic site labels (<code>crystLabel</code>) of the atoms in this view. Use this to serialise a selection in a way that is robust to atom reordering; restore with Model#viewFromLabels.</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line463">line 463</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">Array.&lt;string></span></dd></dl></div><h3 class="name has-anchor" id="uniqueSites"><span class="type-signature"></span>uniqueSites<span class="signature">()</span></h3><div class="description"><p>Unique atoms in the current view (based on site labels)</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line215">line 215</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="xor"><span class="type-signature"></span>xor<span class="signature">(mview)</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Exclusive OR with another ModelView</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>mview</code></td><td class="type"><span class="param-type">ModelView</span></td><td class="description last"><p>Other view</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line186">line 186</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Result</p></div><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>