3dmol

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JavaScript/TypeScript molecular visualization library

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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><header><h1 id="AtomSpec-title" class="has-anchor">AtomSpec</h1></header><article><div class="container-overview"><div class="description"><p>Atom representation. Depending on the input file format, not all fields may be defined.</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl></div><h2 id="members" class="subsection-title has-anchor">Members</h2><h3 class="name has-anchor" id="atom"><span class="type-signature"></span>atom<span class="type-signature"> :string</span></h3><div class="description"><p>Atom name; may be more specific than 'elem' (e.g 'CA' for alpha carbon)</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="b"><span class="type-signature"></span>b<span class="type-signature"> :number</span></h3><div class="description"><p>Atom b factor data</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">number</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="bondOrder"><span class="type-signature"></span>bondOrder<span class="type-signature"> :Array</span></h3><div class="description"><p>Array of this atom's bond orders, corresponding to bonds identfied by 'bonds'</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="bondStyles"><span class="type-signature"></span>bondStyles<span class="type-signature"> :Array</span></h3><div class="description"><p>custom bond styling by position in bonds</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="bonds"><span class="type-signature"></span>bonds<span class="type-signature"> :Array</span></h3><div class="description"><p>Array of atom ids this atom is bonded to</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Array</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="callback"><span class="type-signature"></span>callback<span class="type-signature"> :function</span></h3><div class="description"><p>Callback click handler function to be executed on this atom and its parent viewer</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">function</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="chain"><span class="type-signature"></span>chain<span class="type-signature"> :string</span></h3><div class="description"><p>Chain this atom belongs to, if specified in input file (e.g 'A' for chain A)</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="clickable"><span class="type-signature"></span>clickable<span class="type-signature"> :boolean</span></h3><div class="description"><p>Set this flag to true to enable click selection handling for this atom</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="color"><span class="type-signature"></span>color<span class="type-signature"> :<a href="global.html#ColorSpec">ColorSpec</a></span></h3><div class="description"><p>Atom's color, as hex code or built-in color string</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type"><a href="global.html#ColorSpec">ColorSpec</a></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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="elem"><span class="type-signature"></span>elem<span class="type-signature"> :string</span></h3><div class="description"><p>Element abbreviation (e.g. 'H', 'Ca', etc)</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="hetflag"><span class="type-signature"></span>hetflag<span class="type-signature"> :boolean</span></h3><div class="description"><p>Set to true if atom is a heteroatom</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="hover_callback"><span class="type-signature"></span>hover_callback<span class="type-signature"> :function</span></h3><div class="description"><p>Callback hover handler function to be executed on this atom and its parent viewer</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">function</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="hoverable"><span class="type-signature"></span>hoverable<span class="type-signature"> :boolean</span></h3><div class="description"><p>Set this flag to true to enable hover selection handling for this atom</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="index"><span class="type-signature"></span>index<span class="type-signature"> :number</span></h3><div class="description"><p>Index of atom in molecule</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">number</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="invert"><span class="type-signature"></span>invert<span class="type-signature"> :boolean</span></h3><div class="description"><p>for selection, inverts the meaning of the selection</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="lchain"><span class="type-signature"></span>lchain<span class="type-signature"> :string</span></h3><div class="description"><p>Label chain (not author)</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="lresi"><span class="type-signature"></span>lresi<span class="type-signature"> :number</span></h3><div class="description"><p>Label residues number (not author)</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">number</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="lresn"><span class="type-signature"></span>lresn<span class="type-signature"> :string</span></h3><div class="description"><p>Residue label name</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="pdbline"><span class="type-signature"></span>pdbline<span class="type-signature"> :string</span></h3><div class="description"><p>If applicable, this atom's record entry from the input PDB file (used to output new PDB from models)</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="properties"><span class="type-signature"></span>properties<span class="type-signature"> :Record.<string, any></span></h3><div class="description"><p>Optional mapping of additional properties</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Record.<string, any></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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="resi"><span class="type-signature"></span>resi<span class="type-signature"> :number</span></h3><div class="description"><p>Residue number</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">number</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="resn"><span class="type-signature"></span>resn<span class="type-signature"> :string</span></h3><div class="description"><p>Parent residue name</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="serial"><span class="type-signature"></span>serial<span class="type-signature"> :number</span></h3><div class="description"><p>Atom's serial id number</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">number</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="singleBonds"><span class="type-signature"></span>singleBonds<span class="type-signature"> :boolean</span></h3><div class="description"><p>true if this atom forms only single bonds or no bonds at all</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="ss"><span class="type-signature"></span>ss<span class="type-signature"> :string</span></h3><div class="description"><p>Secondary structure identifier (for cartoon render; e.g. 'h' for helix)</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="style"><span class="type-signature"></span>style<span class="type-signature"> :<a href="AtomStyleSpec.html">AtomStyleSpec</a></span></h3><div class="description"><p>style of atom</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type"><a href="AtomStyleSpec.html">AtomStyleSpec</a></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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="surfaceColor"><span class="type-signature"></span>surfaceColor<span class="type-signature"> :<a href="global.html#ColorSpec">ColorSpec</a></span></h3><div class="description"><p>Hex code for color to be used for surface patch over this atom</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type"><a href="global.html#ColorSpec">ColorSpec</a></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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="unhover_callback"><span class="type-signature"></span>unhover_callback<span class="type-signature"> :function</span></h3><div class="description"><p>Callback handling "unhover" to be executed on this atom and its parent viewer</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">function</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="x"><span class="type-signature"></span>x<span class="type-signature"> :number</span></h3><div class="description"><p>Atom's x coordinate</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">number</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="y"><span class="type-signature"></span>y<span class="type-signature"> :number</span></h3><div class="description"><p>Atom's y coordinate</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">number</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="specs.ts.html">specs.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="z"><span class="type-signature"></span>z<span class="type-signature"> :number</span></h3><div class="description"><p>Atom's z coordinate</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">number</span></li></ul></div><dl class="details"><div 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