UNPKG

crystvis-js

Version:

A Three.js based crystallographic visualisation tool

3,267 lines (960 loc) 74.2 kB
<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <!-- Adding favicon --> <!-- Adding meta --> <!-- Adding external script--> <!-- Adding external style--> <!-- Adding scripts--> <!-- Adding style--> <!-- Adding overlay script--> <!-- Adding overlay style--> <title> AtomImage </title> <!--[if lt IE 9]> <script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script> <![endif]--> <link type="text/css" rel="stylesheet" href="styles/third-party/ionicons.min.css"> <link type="text/css" rel="stylesheet" href="styles/third-party/prettify-tomorrow.css"> <link type="text/css" rel="stylesheet" href="styles/reset.css"> <link type="text/css" rel="stylesheet" href="styles/clean-jsdoc-theme-base.css"> <link type="text/css" rel="stylesheet" href="styles/clean-jsdoc-theme-dark.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="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> </defs> </svg> </head> <body> <nav class="navbar" id="navbar"> <div class="navbar-heading" id="navbar-heading"><a href="index.html"><h2 class="navbar-heading-text">Home</h2></a></div><div class="search-box" id="search-box"><div class="search-box-input-container"><input class="search-box-input" type="text" placeholder="Search..." id="search-box-input" /><svg class="search-icon" alt="search-icon"><use xlink:href="#search-icon"></use></svg></div><div class="search-item-container" id="search-item-container"><ul class="search-item-ul" id="search-item-ul"></ul></div></div><div class="sidebar-main-content" id="sidebar-main-content"><div class="accordion collapsed" id="9953002" > <h3 class="accordion-heading">Modules<svg><use xlink:href="#down-icon"></use></svg></h3><ul class="accordion-content"><li class="accordion-list" id=""><a href="lib_model.module_js.html">lib/model.js</a></li><li class="accordion-list" id=""><a href="lib_modelview.module_js.html">lib/modelview.js</a></li><li class="accordion-list" id=""><a href="lib_visualizer.module_js.html">lib/visualizer.js</a></li></ul> </div><div class="accordion collapsed" id="3878701" > <h3 class="accordion-heading">Classes<svg><use xlink:href="#down-icon"></use></svg></h3><ul class="accordion-content"><li class="accordion collapsed child" id=6175172><div class="accordion-heading child"><a href="lib_model.module_js-AtomImage.html">AtomImage</a><svg><use xlink:href="#down-icon"></use></svg></div><ul class='methods accordion-content'><li data-type='method'><a href="lib_model.module_js-AtomImage.html#addEllipsoid">addEllipsoid</a></li><li data-type='method'><a href="lib_model.module_js-AtomImage.html#addLabel">addLabel</a></li><li data-type='method'><a href="lib_model.module_js-AtomImage.html#ellipsoidProperty">ellipsoidProperty</a></li><li data-type='method'><a href="lib_model.module_js-AtomImage.html#getArrayValue">getArrayValue</a></li><li data-type='method'><a href="lib_model.module_js-AtomImage.html#labelProperty">labelProperty</a></li><li data-type='method'><a href="lib_model.module_js-AtomImage.html#removeEllipsoid">removeEllipsoid</a></li><li data-type='method'><a href="lib_model.module_js-AtomImage.html#removeLabel">removeLabel</a></li></ul></li><li class="accordion-list" id=""><a href="lib_model.module_js-BondImage.html">BondImage</a></li><li class="accordion collapsed child" id=6715610><div class="accordion-heading child"><a href="lib_model.module_js-Model.html">Model</a><svg><use xlink:href="#down-icon"></use></svg></div><ul class='methods accordion-content'><li data-type='method'><a href="lib_model.module_js-Model.html#absToFrac">absToFrac</a></li><li data-type='method'><a href="lib_model.module_js-Model.html#addLink">addLink</a></li><li data-type='method'><a href="lib_model.module_js-Model.html#addSphere">addSphere</a></li><li data-type='method'><a href="lib_model.module_js-Model.html#clearGraphics">clearGraphics</a></li><li data-type='method'><a href="lib_model.module_js-Model.html#deleteArray">deleteArray</a></li><li data-type='method'><a href="lib_model.module_js-Model.html#find">find</a></li><li data-type='method'><a href="lib_model.module_js-Model.html#fracToAbs">fracToAbs</a></li><li data-type='method'><a href="lib_model.module_js-Model.html#getArray">getArray</a></li><li data-type='method'><a href="lib_model.module_js-Model.html#hasArray">hasArray</a></li><li data-type='method'><a href="lib_model.module_js-Model.html#minimumSupercell">minimumSupercell</a></li><li data-type='method'><a href="lib_model.module_js-Model.html#removeGraphics">removeGraphics</a></li><li data-type='method'><a href="lib_model.module_js-Model.html#setArray">setArray</a></li><li data-type='method'><a href="lib_model.module_js-Model.html#view">view</a></li></ul></li><li class="accordion collapsed child" id=2271872><div class="accordion-heading child"><a href="lib_modelview.module_js-ModelView.html">ModelView</a><svg><use xlink:href="#down-icon"></use></svg></div><ul class='methods accordion-content'><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#addEllipsoids">addEllipsoids</a></li><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#addLabels">addLabels</a></li><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#and">and</a></li><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#ellipsoidProperties">ellipsoidProperties</a></li><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#find">find</a></li><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#hide">hide</a></li><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#labelProperties">labelProperties</a></li><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#map">map</a></li><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#not">not</a></li><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#or">or</a></li><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#removeEllipsoids">removeEllipsoids</a></li><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#removeLabels">removeLabels</a></li><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#setProperty">setProperty</a></li><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#show">show</a></li><li data-type='method'><a href="lib_modelview.module_js-ModelView.html#xor">xor</a></li></ul></li><li class="accordion collapsed child" id=6565660><div class="accordion-heading child"><a href="lib_visualizer.module_js-CrystVis.html">CrystVis</a><svg><use xlink:href="#down-icon"></use></svg></div><ul class='methods accordion-content'><li data-type='method'><a href="lib_visualizer.module_js-CrystVis.html#addPrimitive">addPrimitive</a></li><li data-type='method'><a href="lib_visualizer.module_js-CrystVis.html#centerCamera">centerCamera</a></li><li data-type='method'><a href="lib_visualizer.module_js-CrystVis.html#deleteModel">deleteModel</a></li><li data-type='method'><a href="lib_visualizer.module_js-CrystVis.html#displayModel">displayModel</a></li><li data-type='method'><a href="lib_visualizer.module_js-CrystVis.html#getScreenshotData">getScreenshotData</a></li><li data-type='method'><a href="lib_visualizer.module_js-CrystVis.html#loadModels">loadModels</a></li><li data-type='method'><a href="lib_visualizer.module_js-CrystVis.html#onAtomBox">onAtomBox</a></li><li data-type='method'><a href="lib_visualizer.module_js-CrystVis.html#onAtomClick">onAtomClick</a></li><li data-type='method'><a href="lib_visualizer.module_js-CrystVis.html#reloadModel">reloadModel</a></li><li data-type='method'><a href="lib_visualizer.module_js-CrystVis.html#removePrimitive">removePrimitive</a></li></ul></li></ul> </div><div class="accordion collapsed" id="6000571" > <h3 class="accordion-heading">Tutorials<svg><use xlink:href="#down-icon"></use></svg></h3><ul class="accordion-content"><li class="accordion-list" id=""><a href="tutorial-Events.html">Events</a></li><li class="accordion-list" id=""><a href="tutorial-Queries.html">Queries</a></li></ul> </div> </nav> <div class="navbar-ham" id="navbar-ham"> <div> <div class="first"></div> <div class="second"></div> <div class="third"></div> </div> </div> <div id="main" class="main-content"> <h1 id='page-title' class="page-title"> AtomImage </h1> <section> <header> <h2> <span class="ancestors"><a href="lib_model.module_js.html">lib/model.js</a>~</span> AtomImage </h2> <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>Constructor</h2> <h4 class="name" id="AtomImage"> <a href="#AtomImage">#</a> <span class="type-signature"></span>new AtomImage<span class="signature">(model, index, ijk)</span><span class="type-signature"></span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line32">line 32</a> </li></ul></dd> </div> </dl> </div> <h3 class="subsection-title">Members</h3> <h4 class="name" id="aura"> <a href="#aura">#</a> <span class="type-signature">(readonly) </span>aura<span class="type-signature"> :AuraMesh</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line364">line 364</a> </li></ul></dd> </div> </dl> <h4 class="name" id="baseRadius"> <a href="#baseRadius">#</a> <span class="type-signature"></span>baseRadius<span class="type-signature"> :float</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line418">line 418</a> </li></ul></dd> </div> </dl> <h4 class="name" id="bondedAtoms"> <a href="#bondedAtoms">#</a> <span class="type-signature">(readonly) </span>bondedAtoms<span class="type-signature"> :Array.&lt;AtomImage></span> </h4> <div class="description"> <p>All atoms bonded to this atom</p> </div> <div class="member-item-container flex"> <strong>Type: </strong> <ul> <li> <span class="param-type">Array.&lt;AtomImage></span> </li> </ul> </div> <dl class="details"> <div class="details-item-container"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line282">line 282</a> </li></ul></dd> </div> </dl> <h4 class="name" id="bonds"> <a href="#bonds">#</a> <span class="type-signature">(readonly) </span>bonds<span class="type-signature"> :Array.&lt;BondImage></span> </h4> <div class="description"> <p>All bonds connected to this atom</p> </div> <div class="member-item-container flex"> <strong>Type: </strong> <ul> <li> <span class="param-type">Array.&lt;BondImage></span> </li> </ul> </div> <dl class="details"> <div class="details-item-container"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line273">line 273</a> </li></ul></dd> </div> </dl> <h4 class="name" id="bondsFrom"> <a href="#bondsFrom">#</a> <span class="type-signature">(readonly) </span>bondsFrom<span class="type-signature"> :Array.&lt;BondImage></span> </h4> <div class="description"> <p>Bonds from this atom</p> </div> <div class="member-item-container flex"> <strong>Type: </strong> <ul> <li> <span class="param-type">Array.&lt;BondImage></span> </li> </ul> </div> <dl class="details"> <div class="details-item-container"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line255">line 255</a> </li></ul></dd> </div> </dl> <h4 class="name" id="bondsTo"> <a href="#bondsTo">#</a> <span class="type-signature">(readonly) </span>bondsTo<span class="type-signature"> :Array.&lt;BondImage></span> </h4> <div class="description"> <p>Bonds to this atom</p> </div> <div class="member-item-container flex"> <strong>Type: </strong> <ul> <li> <span class="param-type">Array.&lt;BondImage></span> </li> </ul> </div> <dl class="details"> <div class="details-item-container"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line264">line 264</a> </li></ul></dd> </div> </dl> <h4 class="name" id="color"> <a href="#color">#</a> <span class="type-signature"></span>color<span class="type-signature"> :int</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line467">line 467</a> </li></ul></dd> </div> </dl> <h4 class="name" id="cpkColor"> <a href="#cpkColor">#</a> <span class="type-signature">(readonly) </span>cpkColor<span class="type-signature"> :int</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line237">line 237</a> </li></ul></dd> </div> </dl> <h4 class="name" id="crystLabel"> <a href="#crystLabel">#</a> <span class="type-signature">(readonly) </span>crystLabel<span class="type-signature"> :String</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line162">line 162</a> </li></ul></dd> </div> </dl> <h4 class="name" id="element"> <a href="#element">#</a> <span class="type-signature">(readonly) </span>element<span class="type-signature"> :String</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line153">line 153</a> </li></ul></dd> </div> </dl> <h4 class="name" id="elementData"> <a href="#elementData">#</a> <span class="type-signature">(readonly) </span>elementData<span class="type-signature"> :Object</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line171">line 171</a> </li></ul></dd> </div> </dl> <h4 class="name" id="fxyz"> <a href="#fxyz">#</a> <span class="type-signature">(readonly) </span>fxyz<span class="type-signature"> :Array.&lt;float></span> </h4> <div class="description"> <p>Fractional coordinates of this atom image</p> </div> <div class="member-item-container flex"> <strong>Type: </strong> <ul> <li> <span class="param-type">Array.&lt;float></span> </li> </ul> </div> <dl class="details"> <div class="details-item-container"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line332">line 332</a> </li></ul></dd> </div> </dl> <h4 class="name" id="fxyz0"> <a href="#fxyz0">#</a> <span class="type-signature">(readonly) </span>fxyz0<span class="type-signature"> :Array.&lt;float></span> </h4> <div class="description"> <p>Fractional coordinates of this atom's original</p> </div> <div class="member-item-container flex"> <strong>Type: </strong> <ul> <li> <span class="param-type">Array.&lt;float></span> </li> </ul> </div> <dl class="details"> <div class="details-item-container"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line323">line 323</a> </li></ul></dd> </div> </dl> <h4 class="name" id="highlighted"> <a href="#highlighted">#</a> <span class="type-signature"></span>highlighted<span class="type-signature"> :bool</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line524">line 524</a> </li></ul></dd> </div> </dl> <h4 class="name" id="id"> <a href="#id">#</a> <span class="type-signature">(readonly) </span>id<span class="type-signature"> :String</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line126">line 126</a> </li></ul></dd> </div> </dl> <h4 class="name" id="ijk"> <a href="#ijk">#</a> <span class="type-signature">(readonly) </span>ijk<span class="type-signature"> :Array.&lt;int></span> </h4> <div class="description"> <p>Cell indices of this atom image</p> </div> <div class="member-item-container flex"> <strong>Type: </strong> <ul> <li> <span class="param-type">Array.&lt;int></span> </li> </ul> </div> <dl class="details"> <div class="details-item-container"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line296">line 296</a> </li></ul></dd> </div> </dl> <h4 class="name" id="imgIndex"> <a href="#imgIndex">#</a> <span class="type-signature">(readonly) </span>imgIndex<span class="type-signature"> :int</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line135">line 135</a> </li></ul></dd> </div> </dl> <h4 class="name" id="index"> <a href="#index">#</a> <span class="type-signature">(readonly) </span>index<span class="type-signature"> :int</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line117">line 117</a> </li></ul></dd> </div> </dl> <h4 class="name" id="isotope"> <a href="#isotope">#</a> <span class="type-signature"></span>isotope<span class="type-signature"> :int</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line191">line 191</a> </li></ul></dd> </div> </dl> <h4 class="name" id="isotopeData"> <a href="#isotopeData">#</a> <span class="type-signature">(readonly) </span>isotopeData<span class="type-signature"> :Object</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line180">line 180</a> </li></ul></dd> </div> </dl> <h4 class="name" id="isotopeGlobal"> <a href="#isotopeGlobal">#</a> <span class="type-signature"></span>isotopeGlobal<span class="type-signature"> :int</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line209">line 209</a> </li></ul></dd> </div> </dl> <h4 class="name" id="mesh"> <a href="#mesh">#</a> <span class="type-signature">(readonly) </span>mesh<span class="type-signature"> :AtomMesh</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line350">line 350</a> </li></ul></dd> </div> </dl> <h4 class="name" id="model"> <a href="#model">#</a> <span class="type-signature">(readonly) </span>model<span class="type-signature"> :Model</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line93">line 93</a> </li></ul></dd> </div> </dl> <h4 class="name" id="moleculeIndex"> <a href="#moleculeIndex">#</a> <span class="type-signature">(readonly) </span>moleculeIndex<span class="type-signature"> :int</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line341">line 341</a> </li></ul></dd> </div> </dl> <h4 class="name" id="number"> <a href="#number">#</a> <span class="type-signature">(readonly) </span>number<span class="type-signature"> :int</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line226">line 226</a> </li></ul></dd> </div> </dl> <h4 class="name" id="opacity"> <a href="#opacity">#</a> <span class="type-signature"></span>opacity<span class="type-signature"> :float</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line499">line 499</a> </li></ul></dd> </div> </dl> <h4 class="name" id="radius"> <a href="#radius">#</a> <span class="type-signature"></span>radius<span class="type-signature"> :float</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line452">line 452</a> </li></ul></dd> </div> </dl> <h4 class="name" id="renderer"> <a href="#renderer">#</a> <span class="type-signature">(readonly) </span>renderer<span class="type-signature"> :Renderer</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line102">line 102</a> </li></ul></dd> </div> </dl> <h4 class="name" id="scale"> <a href="#scale">#</a> <span class="type-signature"></span>scale<span class="type-signature"> :float</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line435">line 435</a> </li></ul></dd> </div> </dl> <h4 class="name" id="speciesIndex"> <a href="#speciesIndex">#</a> <span class="type-signature">(readonly) </span>speciesIndex<span class="type-signature"> :int</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line144">line 144</a> </li></ul></dd> </div> </dl> <h4 class="name" id="vdwRadius"> <a href="#vdwRadius">#</a> <span class="type-signature">(readonly) </span>vdwRadius<span class="type-signature"> :float</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line246">line 246</a> </li></ul></dd> </div> </dl> <h4 class="name" id="visible"> <a href="#visible">#</a> <span class="type-signature"></span>visible<span class="type-signature"> :bool</span> </h4> <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">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line383">line 383</a> </li></ul></dd> </div> </dl> <h4 class="name" id="xyz"> <a href="#xyz">#</a> <span class="type-signature">(readonly) </span>xyz<span class="type-signature"> :Array.&lt;float></span> </h4> <div class="description"> <p>Position of this atom image</p> </div> <div class="member-item-container flex"> <strong>Type: </strong> <ul> <li> <span class="param-type">Array.&lt;float></span> </li> </ul> </div> <dl class="details"> <div class="details-item-container"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line314">line 314</a> </li></ul></dd> </div> </dl> <h4 class="name" id="xyz0"> <a href="#xyz0">#</a> <span class="type-signature">(readonly) </span>xyz0<span class="type-signature"> :Array.&lt;float></span> </h4> <div class="description"> <p>Position of this atom's original</p> </div> <div class="member-item-container flex"> <strong>Type: </strong> <ul> <li> <span class="param-type">Array.&lt;float></span> </li> </ul> </div> <dl class="details"> <div class="details-item-container"> <dt class="tag-source">Source:</dt> <dd class="tag-source"><ul class="dummy"><li> <a href="model.js.html">model.js</a>, <a href="model.js.html#line305">line 305</a> </li></ul></dd> </div> </dl> <h3 class="subsection-title">Methods</h3> <h4 class="name" id="addEllipsoid"> <a href="#addEllipsoid">#</a> <span class="type-signature"></span>addEllipsoid<span class="signature">(data, name, parameters)</span><span class="type-signature"></span> </h4> <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> | <span class="param-type">Object</span> | <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>Nam