3dmol
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JavaScript/TypeScript molecular visualization library
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href="global.html#ssColors">ssColors</a></div><div class="sidebar-section-children"><a href="global.html#syncSurface">syncSurface</a></div><div class="sidebar-section-children"><a href="global.html#viewers">viewers</a></div></div></div></div></div><div class="navbar-container" id="VuAckcnZhf"><nav class="navbar"><div class="navbar-left-items"><div class="navbar-item"><a id="" href="https://3dmol.org/doc/index.html" target="">Documentation</a></div><div class="navbar-item"><a id="" href="tutorial-home.html" target="">Tutorials</a></div><div class="navbar-item"><a id="" href="https://github.com/3dmol/3Dmol.js" target="_blank">GitHub</a></div></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="#dark-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><article><div class="container-overview"></div><h2 id="members" class="subsection-title has-anchor">Members</h2><h3 class="name has-anchor" id="CAP"><span class="type-signature">(readonly) </span>CAP<span class="type-signature"></span></h3><div class="description"><p>Enum for cylinder cap styles.</p></div><b class="subsection-title">Properties</b><div class="allow-overflow"><table class="props"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>NONE</code></td><td class="type"></td><td class="description last"></td></tr><tr><td class="name"><code>FLAT</code></td><td class="type"></td><td class="description last"></td></tr><tr><td class="name"><code>ROUND</code></td><td class="type"></td><td class="description last"></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="GLDraw.ts.html">GLDraw.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="OFFSETS"><span class="type-signature">(constant) </span>OFFSETS<span class="type-signature"></span></h3><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="parsers_utils_assignBonds.ts.html">parsers/utils/assignBonds.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="SurfaceType"><span class="type-signature">(readonly) </span>SurfaceType<span class="type-signature"> :number</span></h3><div class="description"><p>Surface types</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">number</span></li></ul></div><b class="subsection-title">Properties</b><div class="allow-overflow"><table class="props"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>VDW</code></td><td class="type"></td><td class="description last"><p>van der Waals surface</p></td></tr><tr><td class="name"><code>MS</code></td><td class="type"></td><td class="description last"><p>Molecular surface</p></td></tr><tr><td class="name"><code>SAS</code></td><td class="type"></td><td class="description last"><p>Solvent accessible surface</p></td></tr><tr><td class="name"><code>SES</code></td><td class="type"></td><td class="description last"><p>Solvent exposed surface</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="ProteinSurface4.ts.html">ProteinSurface4.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="builtinColorSchemes"><span class="type-signature">(constant) </span>builtinColorSchemes<span class="type-signature"></span></h3><div class="description"><p>built in color schemes<br>The user can pass these strings directly as the colorscheme</p></div><b class="subsection-title">Properties</b><div class="allow-overflow"><table class="props"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>ssPyMol</code></td><td class="type"></td><td class="description last"><p>pymol secondary structure</p></td></tr><tr><td class="name"><code>ssJmol</code></td><td class="type"></td><td class="description last"><p>jmol secondary structure</p></td></tr><tr><td class="name"><code>Jmol</code></td><td class="type"></td><td class="description last"><p>jmol element defaults</p></td></tr><tr><td class="name"><code>amino</code></td><td class="type"></td><td class="description last"><p>amino acid coloring</p></td></tr><tr><td class="name"><code>shapely</code></td><td class="type"></td><td class="description last"><p>amino acid coloring</p></td></tr><tr><td class="name"><code>nucleic</code></td><td class="type"></td><td class="description last"><p>nucleic acid coloring</p></td></tr><tr><td class="name"><code>chain</code></td><td class="type"></td><td class="description last"><p>color by chain</p></td></tr><tr><td class="name"><code>rasmol</code></td><td class="type"></td><td class="description last"><p>rasmol default element coloring</p></td></tr><tr><td class="name"><code>default</code></td><td class="type"></td><td class="description last"><p>default element coloring</p></td></tr><tr><td class="name"><code>greenCarbon</code></td><td class="type"></td><td class="description last"><p>default element coloring with green carbon</p></td></tr><tr><td class="name"><code>cyanCarbon</code></td><td class="type"></td><td class="description last"><p>default element coloring with cyan carbon</p></td></tr><tr><td class="name"><code>magentaCarbon</code></td><td class="type"></td><td class="description last"><p>default element coloring with magenta carbon</p></td></tr><tr><td class="name"><code>purpleCarbon</code></td><td class="type"></td><td class="description last"><p>default element coloring with purple carbon</p></td></tr><tr><td class="name"><code>whiteCarbon</code></td><td class="type"></td><td class="description last"><p>default element coloring with white carbon</p></td></tr><tr><td class="name"><code>orangeCarbon</code></td><td class="type"></td><td class="description last"><p>default element coloring with orange carbon</p></td></tr><tr><td class="name"><code>yellowCarbon</code></td><td class="type"></td><td class="description last"><p>default element coloring with yellow carbon</p></td></tr><tr><td class="name"><code>blueCarbon</code></td><td class="type"></td><td class="description last"><p>default element coloring with blue carbon</p></td></tr><tr><td class="name"><code>chainHetatm</code></td><td class="type"></td><td class="description last"><p>color chains</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="colors.ts.html">colors.ts</a></li></ul></dd></div></dl><b>Example</b><div class="rel"><pre class="prettyprint"><code>window.$3Dmol.download("pdb:4UAA",viewer,{},function(){
viewer.setBackgroundColor(0xffffffff);
var colorAsSnake = function(atom) {
return atom.resi % 2 ? 'white': 'green'
};
viewer.setStyle( {chain:'A'}, { cartoon: {colorfunc: colorAsSnake }});
viewer.setStyle( {chain:'B'}, { stick: {colorscheme: 'yellowCarbon'}});
viewer.render();
});</code></pre></div><h3 class="name has-anchor" id="builtinGradients"><span class="type-signature">(constant) </span>builtinGradients<span class="type-signature"></span></h3><div class="description"><p>built in gradient schemes<br>The user can pass these strings directly as the gradient</p></div><b class="subsection-title">Properties</b><div class="allow-overflow"><table class="props"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>rwb</code></td><td class="type"></td><td class="description last"><p>red/white/blue, supports setting a mid point for white</p></td></tr><tr><td class="name"><code>roygb</code></td><td class="type"></td><td class="description last"><p>rainbow</p></td></tr><tr><td class="name"><code>sinebow</code></td><td class="type"></td><td class="description last"><p>rainbow with better saturation properties</p></td></tr><tr><td class="name"><code>linear</code></td><td class="type"></td><td class="description last"><p>linearly maps between provided colors</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="Gradient.ts.html">Gradient.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="dic"><span class="type-signature">(constant) </span>dic<span class="type-signature"></span></h3><div class="description"><p>Parse a lammps trajectory file from str and create atoms</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="parsers_LAMMPSTRJ.ts.html">parsers/LAMMPSTRJ.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="elementColors"><span class="type-signature">(constant) </span>elementColors<span class="type-signature"></span></h3><div class="description"><p>Preset element coloring - from individual element colors to entire mappings (e.g. 'elementColors.Jmol' colors atoms with Jmol stylings)</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="colors.ts.html">colors.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="ssColors"><span class="type-signature">(constant) </span>ssColors<span class="type-signature"></span></h3><div class="description"><p>Preset secondary structure color scheme</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="colors.ts.html">colors.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="syncSurface"><span class="type-signature"></span>syncSurface<span class="type-signature"> :boolean</span></h3><div class="description"><p>Render surface synchronously if true</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">boolean</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="ProteinSurface4.ts.html">ProteinSurface4.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="viewers"><span class="type-signature"></span>viewers<span class="type-signature"></span></h3><div class="description"><p>Contains a dictionary of embedded viewers created from HTML elements<br>with a the viewer_3Dmoljs css class indexed by their id (or numerically<br>if they do not have an id).</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="autoload.ts.html">autoload.ts</a></li></ul></dd></div></dl><h2 id="methods" class="subsection-title has-anchor">Methods</h2><h3 class="name has-anchor" id="BCIF"><span class="type-signature"></span>BCIF<span class="signature">(bindata, ParserOptionsSpec)</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>bindata</code></td><td class="type"></td><td class="description last"><p>binary UInt8Array buffer or a base64 encoded string</p></td></tr><tr><td class="name"><code>ParserOptionsSpec</code></td><td class="type"></td><td class="description last"></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="parsers_BCIF.ts.html">parsers/BCIF.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="CDJSON"><span class="type-signature"></span>CDJSON<span class="signature">(str, options)</span></h3><div class="description"><p>This parses the ChemDoodle json file format. Although this is registered<br>for the json file extension, other chemical json file formats exist that<br>this can not parse. Check which one you have and do not assume that<br>.json can be parsed</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>str</code></td><td class="type"><span class="param-type">string</span></td><td class="description last"></td></tr><tr><td class="name"><code>options</code></td><td class="type"><span class="param-type"><a href="ParserOptionsSpec.html">ParserOptionsSpec</a></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="parsers_CDJSON.ts.html">parsers/CDJSON.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="CIF"><span class="type-signature"></span>CIF<span class="signature">(str, options)</span></h3><div class="description"><p>Puts atoms specified in mmCIF fromat in str into atoms</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>str</code></td><td class="type"><span class="param-type">string</span></td><td class="description last"></td></tr><tr><td class="name"><code>options</code></td><td class="type"><span class="param-type"><a href="ParserOptionsSpec.html">ParserOptionsSpec</a></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="parsers_CIF.ts.html">parsers/CIF.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="CUBE"><span class="type-signature"></span>CUBE<span class="signature">(str, options)</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>str</code></td><td class="type"><span class="param-type">string</span></td><td class="description last"></td></tr><tr><td class="name"><code>options</code></td><td class="type"><span class="param-type"><a href="ParserOptionsSpec.html">ParserOptionsSpec</a></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="parsers_CUBE.ts.html">parsers/CUBE.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="GRO"><span class="type-signature"></span>GRO<span class="signature">(str, options)</span><span class="type-signature"> → {Array.<Array.<<a href="AtomSpec.html">AtomSpec</a>>>}</span></h3><div class="description"><p>Parse a gro file from str and create atoms</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>str</code></td><td class="type"><span class="param-type">string</span></td><td class="description last"></td></tr><tr><td class="name"><code>options</code></td><td class="type"><span class="param-type"><a href="ParserOptionsSpec.html">ParserOptionsSpec</a></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="parsers_GRO.ts.html">parsers/GRO.ts</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><ul><li>Returns a 2D array of type AtomSpec</li></ul></div><dl class="param-type"><dt>Type: </dt><dd><span class="param-type">Array.<Array.<<a href="AtomSpec.html">AtomSpec</a>>></span></dd></dl></div><h3 class="name has-anchor" id="MMTFparser"><span class="type-signature"></span>MMTFparser<span class="signature">(bindata, ParserOptionsSpec)</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>bindata</code></td><td class="type"></td><td class="description last"><p>binary UInt8Array buffer or a base64 encoded string</p></td></tr><tr><td class="name"><code>ParserOptionsSpec</code></td><td class="type"></td><td class="description last"></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="parsers_MMTF.ts.html">parsers/MMTF.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="MOL2"><span class="type-signature"></span>MOL2<span class="signature">(str, options)</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>str</code></td><td class="type"><span class="param-type">string</span></td><td class="description last"></td></tr><tr><td class="name"><code>options</code></td><td class="type"><span class="param-type"><a href="ParserOptionsSpec.html">ParserOptionsSpec</a></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="parsers_MOL2.ts.html">parsers/MOL2.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="PDB"><span class="type-signature"></span>PDB<span class="signature">(str, options)</span></h3><div class="description"><p>Parse pdb file from str and create atoms if computeStruct is true will always perform secondary structure analysis,<br>otherwise only do analysis of SHEET/HELIX comments are missing</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>str</code></td><td class="type"><span class="param-type">string</span></td><td class="description last"></td></tr><tr><td class="name"><code>options</code></td><td class="type"><span class="param-type"><a href="ParserOptionsSpec.html">ParserOptionsSpec</a></span></td><td class="description last"><p>keepH (do not strip hydrogens), noSecondaryStructure,<br>assignbonds (default true, calculate implicit bonds)<br>(do not compute ss), altLoc (which alternate location to select, if present; '*' to load all)</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="parsers_PDB.ts.html">parsers/PDB.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="PQR"><span class="type-signature"></span>PQR<span class="signature">(str, options)</span></h3><div class="description"><p>Parse a pqr file from str and create atoms. A pqr file is assumed to be a whitespace delimited PDB with charge and radius fields.</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>str</code></td><td class="type"><span class="param-type">string</span></td><td class="description last"></td></tr><tr><td class="name"><code>options</code></td><td class="type"><span class="param-type"><a href="ParserOptionsSpec.html">ParserOptionsSpec</a></span></td><td class="description last"><p>noSecondaryStructure (do not compute ss)</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="parsers_PQR.ts.html">parsers/PQR.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="PRMTOP"><span class="type-signature"></span>PRMTOP<span class="signature">(str, options)</span></h3><div class="description"><p>Parse a prmtop file from str and create atoms</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>str</code></td><td class="type"><span class="param-type">string</span></td><td class="description last"></td></tr><tr><td class="name"><code>options</code></td><td class="type"><span class="param-type"><a href="ParserOptionsSpec.html">ParserOptionsSpec</a></span></td><td class="description last"><p>noSecondaryStructure (do not compute ss)</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="parsers_PRMTOP.ts.html">parsers/PRMTOP.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="SDF"><span class="type-signature"></span>SDF<span class="signature">(str, options)</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>str</code></td><td class="type"><span class="param-type">string</span></td><td class="description last"></td></tr><tr><td class="name"><code>options</code></td><td class="type"><span class="param-type"><a href="ParserOptionsSpec.html">ParserOptionsSpec</a></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="parsers_SDF.ts.html">parsers/SDF.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="VASP"><span class="type-signature"></span>VASP<span class="signature">(str, options)</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>str</code></td><td class="type"><span class="param-type">string</span></td><td class="description last"></td></tr><tr><td class="name"><code>options</code></td><td class="type"><span class="param-type"><a href="ParserOptionsSpec.html">ParserOptionsSpec</a></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="parsers_VASP.ts.html">parsers/VASP.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="XYZ"><span class="type-signature"></span>XYZ<span class="signature">(str, options)</span></h3><div class="description"><p>Read an XYZ file from str and return result</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>str</code></td><td class="type"><span class="param-type">string</span></td><td class="description last"></td></tr><tr><td class="name"><code>options</code></td><td class="type"><span class="param-type"><a href="ParserOptionsSpec.html">ParserOptionsSpec</a></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="parsers_XYZ.ts.html">parsers/XYZ.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="assignPDBBonds"><span class="type-signature"></span>assignPDBBonds<span class="signature">(atomsarray)</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>atomsarray</code></td><td class="type"><span class="param-type">Array.<<a href="AtomSpec.html">AtomSpec</a>></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="parsers_utils_assignPDBBonds.ts.html">parsers/utils/assignPDBBonds.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="conversionMatrix3"><span class="type-signature"></span>conversionMatrix3<span class="signature">(a, b, c, alpha, beta, gamma)</span><span class="type-signature"> → {<a href="Matrix3.html">Matrix3</a>}</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>a</code></td><td class="type"><span class="param-type">number</span></td><td class="description last"></td></tr><tr><td class="name"><code>b</code></td><td class="type"><span class="param-type">number</span></td><td class="description last"></td></tr><tr><td class="name"><code>c</code></td><td class="type"><span class="param-type">number</span></td><td class="description last"></td></tr><tr><td class="name"><code>alpha</code></td><td class="type"><span class="param-type">number</span></td><td class="description last"></td></tr><tr><td class="name"><code>beta</code></td><td class="type"><span class="param-type">number</span></td><td class="description last"></td></tr><tr><td class="name"><code>gamma</code></td><td class="type"><span class="param-type">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="WebGL_math_utils_conversionMatrix3.ts.html">WebGL/math/utils/conversionMatrix3.ts</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><dl class="param-type"><dt>Type: </dt><dd><span class="param-type"><a href="Matrix3.html">Matrix3</a></span></dd></dl></div><h3 class="name has-anchor" id="createViewer"><span class="type-signature"></span>createViewer<span class="signature">(element, config<span class="signature-attributes">opt</span>)</span><span class="type-signature"> → {<a href="GLViewer.html">GLViewer</a>}</span></h3><div class="description"><p>Create and initialize an appropriate viewer at supplied HTML element using specification in config</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>Attributes</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>element</code></td><td class="type"><span class="param-type">Object</span> |<wbr> <span class="param-type">string</span></td><td class="attributes"></td><td class="description last"><p>Either HTML element or string identifier</p></td></tr><tr><td class="name"><code>config</code></td><td class="type"><span class="param-type"><a href="ViewerSpec.html">ViewerSpec</a></span></td><td class="attributes"><optional><br></td><td class="description last"><p>Viewer configuration</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="GLViewer.ts.html">GLViewer.ts</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>GLViewer, null if unable to instantiate WebGL</p></div><dl class="param-type"><dt>Type: </dt><dd><span class="param-type"><a href="GLViewer.html">GLViewer</a></span></dd></dl></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Example</strong><div class="rel"><pre class="prettyprint"><code>var viewer = $3Dmol.createViewer(
'gldiv', //id of div to create canvas in
{
defaultcolors: $3Dmol.elementColors.rasmol,
backgroundColor: 'black'
}
);</code></pre></div></div><h3 class="name has-anchor" id="createViewerGrid"><span class="type-signature"></span>createViewerGrid<span class="signature">(element, config<span class="signature-attributes">opt</span>, viewer_config<span class="signature-attributes">opt</span>)</span></h3><div class="description"><p>Create and initialize an appropriate a grid of viewers that share a WebGL canvas</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>Attributes</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>element</code></td><td class="type"><span class="param-type">Object</span> |<wbr> <span class="param-type">string</span></td><td class="attributes"></td><td class="description last"><p>Either HTML element or string identifier</p></td></tr><tr><td class="name"><code>config</code></td><td class="type"><span class="param-type">GridSpec</span></td><td class="attributes"><optional><br></td><td class="description last"><p>grid configuration</p></td></tr><tr><td class="name"><code>viewer_config</code></td><td class="type"><span class="param-type"><a href="ViewerGridSpec.html">ViewerGridSpec</a></span></td><td class="attributes"><optional><br></td><td class="description last"><p>Viewer specification to apply to all subviewers</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="GLViewer.ts.html">GLViewer.ts</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>[[GLViewer]] 2D array of GLViewers</p></div></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Example</strong><div class="rel"><pre class="prettyprint"><code>var viewers = $3Dmol.createViewerGrid(
'gldiv', //id of div to create canvas in
{
rows: 2,
cols: 2,
control_all: true //mouse controls all viewers
},
{ backgroundColor: 'lightgrey' }
);
$3Dmol.get('data/1jpy.cif', function(data) {
var viewer = viewers[0][0];
viewer.addModel(data,'cif');
viewer.setStyle({sphere:{}});
viewer.zoomTo();
viewer.render( );
viewer = viewers[0][1];
viewer.addModel(data,'cif');
viewer.setStyle({stick:{}});
viewer.zoomTo();
viewer.render( );
viewer = viewers[1][0];
viewer.addModel(data,'cif');
viewer.setStyle({cartoon:{color:'spectrum'}});
viewer.zoomTo();
viewer.render( );
viewer = viewers[1][1];
viewer.addModel(data,'cif');
viewer.setStyle({cartoon:{colorscheme:'chain'}});
viewer.zoomTo();
viewer.render();
});</code></pre></div></div><h3 class="name has-anchor" id="decode"><span class="type-signature"></span>decode<span class="signature">()</span></h3><div class="description"><p>Fixed point, delta, RLE, integer packing adopted from https://github.com/rcsb/mmtf-javascript/<br>by Alexander Rose <a href="mailto:alexander.rose@weirdbyte.de">alexander.rose@weirdbyte.de</a>, MIT License, Copyright (c) 2016</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="parsers_cifutils_decoder.ts.html">parsers/cifutils/decoder.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="download"><span class="type-signature"></span>download<span class="signature">(query, viewer, options, callback<span class="signature-attributes">opt</span>)</span><span class="type-signature"> → {<a href="GLModel.html">GLModel</a>}</span></h3><div class="description"><p>Load a PDB/PubChem structure into existing viewer. Automatically calls 'zoomTo' and 'render' on viewer after loading 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>Attributes</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>query</code></td><td class="type"><span class="param-type">string</span></td><td class="attributes"></td><td class="description last"><p>String specifying pdb or pubchem id; must be prefaced with "pdb: " or "cid: ", respectively</p></td></tr><tr><td class="name"><code>viewer</code></td><td class="type"><span class="param-type"><a href="GLViewer.html">GLViewer</a></span></td><td class="attributes"></td><td class="description last"><p>Add new model to existing viewer</p></td></tr><tr><td class="name"><code>options</code></td><td class="type"><span class="param-type">Object</span></td><td class="attributes"></td><td class="description last"><p>Specify additional options<br>format: file format to download, if multiple are available, default format is pdb<br>pdbUri: URI to retrieve PDB files, default URI is http://www.rcsb.org/pdb/files/</p></td></tr><tr><td class="name"><code>callback</code></td><td class="type"><span class="param-type">function</span></td><td class="attributes"><optional><br>