@ccp-nc/crystvis-js

Version:

A Three.js based crystallographic visualisation tool

3 lines • 41.3 kB

HTML

<!DOCTYPE html><html lang="en" style="font-size:16px"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width,initial-scale=1"><title>Class: AtomImage</title><script src="scripts/third-party/hljs.js" defer="defer"></script><script src="scripts/third-party/hljs-line-num.js" defer="defer"></script><script src="scripts/third-party/popper.js" defer="defer"></script><script src="scripts/third-party/tippy.js" defer="defer"></script><script src="scripts/third-party/tocbot.min.js"></script><script>var baseURL="/",locationPathname="";baseURL=(locationPathname=document.location.pathname).substr(0,locationPathname.lastIndexOf("/")+1)</script><link rel="stylesheet" href="styles/clean-jsdoc-theme.min.css"><svg aria-hidden="true" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" style="display:none"><defs><symbol id="copy-icon" viewbox="0 0 488.3 488.3"><g><path d="M314.25,85.4h-227c-21.3,0-38.6,17.3-38.6,38.6v325.7c0,21.3,17.3,38.6,38.6,38.6h227c21.3,0,38.6-17.3,38.6-38.6V124 C352.75,102.7,335.45,85.4,314.25,85.4z M325.75,449.6c0,6.4-5.2,11.6-11.6,11.6h-227c-6.4,0-11.6-5.2-11.6-11.6V124 c0-6.4,5.2-11.6,11.6-11.6h227c6.4,0,11.6,5.2,11.6,11.6V449.6z"/><path d="M401.05,0h-227c-21.3,0-38.6,17.3-38.6,38.6c0,7.5,6,13.5,13.5,13.5s13.5-6,13.5-13.5c0-6.4,5.2-11.6,11.6-11.6h227 c6.4,0,11.6,5.2,11.6,11.6v325.7c0,6.4-5.2,11.6-11.6,11.6c-7.5,0-13.5,6-13.5,13.5s6,13.5,13.5,13.5c21.3,0,38.6-17.3,38.6-38.6 V38.6C439.65,17.3,422.35,0,401.05,0z"/></g></symbol><symbol id="search-icon" viewBox="0 0 512 512"><g><g><path d="M225.474,0C101.151,0,0,101.151,0,225.474c0,124.33,101.151,225.474,225.474,225.474 c124.33,0,225.474-101.144,225.474-225.474C450.948,101.151,349.804,0,225.474,0z M225.474,409.323 c-101.373,0-183.848-82.475-183.848-183.848S124.101,41.626,225.474,41.626s183.848,82.475,183.848,183.848 S326.847,409.323,225.474,409.323z"/></g></g><g><g><path d="M505.902,476.472L386.574,357.144c-8.131-8.131-21.299-8.131-29.43,0c-8.131,8.124-8.131,21.306,0,29.43l119.328,119.328 c4.065,4.065,9.387,6.098,14.715,6.098c5.321,0,10.649-2.033,14.715-6.098C514.033,497.778,514.033,484.596,505.902,476.472z"/></g></g></symbol><symbol id="font-size-icon" viewBox="0 0 24 24"><path fill="none" d="M0 0h24v24H0z"/><path d="M11.246 15H4.754l-2 5H.6L7 4h2l6.4 16h-2.154l-2-5zm-.8-2L8 6.885 5.554 13h4.892zM21 12.535V12h2v8h-2v-.535a4 4 0 1 1 0-6.93zM19 18a2 2 0 1 0 0-4 2 2 0 0 0 0 4z"/></symbol><symbol id="add-icon" viewBox="0 0 24 24"><path fill="none" d="M0 0h24v24H0z"/><path d="M11 11V5h2v6h6v2h-6v6h-2v-6H5v-2z"/></symbol><symbol id="minus-icon" viewBox="0 0 24 24"><path fill="none" d="M0 0h24v24H0z"/><path d="M5 11h14v2H5z"/></symbol><symbol id="dark-theme-icon" viewBox="0 0 24 24"><path fill="none" d="M0 0h24v24H0z"/><path d="M10 7a7 7 0 0 0 12 4.9v.1c0 5.523-4.477 10-10 10S2 17.523 2 12 6.477 2 12 2h.1A6.979 6.979 0 0 0 10 7zm-6 5a8 8 0 0 0 15.062 3.762A9 9 0 0 1 8.238 4.938 7.999 7.999 0 0 0 4 12z"/></symbol><symbol id="light-theme-icon" viewBox="0 0 24 24"><path fill="none" d="M0 0h24v24H0z"/><path d="M12 18a6 6 0 1 1 0-12 6 6 0 0 1 0 12zm0-2a4 4 0 1 0 0-8 4 4 0 0 0 0 8zM11 1h2v3h-2V1zm0 19h2v3h-2v-3zM3.515 4.929l1.414-1.414L7.05 5.636 5.636 7.05 3.515 4.93zM16.95 18.364l1.414-1.414 2.121 2.121-1.414 1.414-2.121-2.121zm2.121-14.85l1.414 1.415-2.121 2.121-1.414-1.414 2.121-2.121zM5.636 16.95l1.414 1.414-2.121 2.121-1.414-1.414 2.121-2.121zM23 11v2h-3v-2h3zM4 11v2H1v-2h3z"/></symbol><symbol id="reset-icon" viewBox="0 0 24 24"><path fill="none" d="M0 0h24v24H0z"/><path d="M18.537 19.567A9.961 9.961 0 0 1 12 22C6.477 22 2 17.523 2 12S6.477 2 12 2s10 4.477 10 10c0 2.136-.67 4.116-1.81 5.74L17 12h3a8 8 0 1 0-2.46 5.772l.997 1.795z"/></symbol><symbol id="down-icon" viewBox="0 0 16 16"><path fill-rule="evenodd" clip-rule="evenodd" d="M12.7803 6.21967C13.0732 6.51256 13.0732 6.98744 12.7803 7.28033L8.53033 11.5303C8.23744 11.8232 7.76256 11.8232 7.46967 11.5303L3.21967 7.28033C2.92678 6.98744 2.92678 6.51256 3.21967 6.21967C3.51256 5.92678 3.98744 5.92678 4.28033 6.21967L8 9.93934L11.7197 6.21967C12.0126 5.92678 12.4874 5.92678 12.7803 6.21967Z"></path></symbol><symbol id="codepen-icon" viewBox="0 0 24 24"><path fill="none" d="M0 0h24v24H0z"/><path d="M16.5 13.202L13 15.535v3.596L19.197 15 16.5 13.202zM14.697 12L12 10.202 9.303 12 12 13.798 14.697 12zM20 10.869L18.303 12 20 13.131V10.87zM19.197 9L13 4.869v3.596l3.5 2.333L19.197 9zM7.5 10.798L11 8.465V4.869L4.803 9 7.5 10.798zM4.803 15L11 19.131v-3.596l-3.5-2.333L4.803 15zM4 13.131L5.697 12 4 10.869v2.262zM2 9a1 1 0 0 1 .445-.832l9-6a1 1 0 0 1 1.11 0l9 6A1 1 0 0 1 22 9v6a1 1 0 0 1-.445.832l-9 6a1 1 0 0 1-1.11 0l-9-6A1 1 0 0 1 2 15V9z"/></symbol><symbol id="close-icon" viewBox="0 0 24 24"><path fill="none" d="M0 0h24v24H0z"/><path d="M12 10.586l4.95-4.95 1.414 1.414-4.95 4.95 4.95 4.95-1.414 1.414-4.95-4.95-4.95 4.95-1.414-1.414 4.95-4.95-4.95-4.95L7.05 5.636z"/></symbol><symbol id="menu-icon" viewBox="0 0 24 24"><path fill="none" d="M0 0h24v24H0z"/><path d="M3 4h18v2H3V4zm0 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.<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.<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.<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.<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.<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.<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.<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.<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.<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.<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.<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.<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.<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.<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.<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.<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.<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.<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#line662">line 662</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"> → {*}</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#line676">line 676</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: </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#line647">line 647</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 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>