3dmol
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JavaScript/TypeScript molecular visualization library
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<html lang="en" style="font-size:16px"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width,initial-scale=1"><meta name="Author" content="David Koes & 3Dmoljs Contributors"><meta name="Description" content="A modern, object-oriented JavaScript library for visualizing molecular data"><title>Interface: ParserOptionsSpec</title><!--[if lt IE 9]>
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Used to specify the options of a GLModel. 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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl></div><h2 id="members" class="subsection-title has-anchor">Members</h2><h3 class="name has-anchor" id="altLoc"><span class="type-signature"></span>altLoc<span class="type-signature"> :string</span></h3><div class="description"><p>which alternate location to select, if present; '*' to load all ; supported by pdb</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="assemblyIndex"><span class="type-signature"></span>assemblyIndex<span class="type-signature"> :number</span></h3><div class="description"><p>index of the assembly in symmetry ; supported by mmtf</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="assignBonds"><span class="type-signature"></span>assignBonds<span class="type-signature"> :boolean</span></h3><div class="description"><p>for formats without explicit bonds (e.g. PDB, xyz) infer bonding (default 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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="doAssembly"><span class="type-signature"></span>doAssembly<span class="type-signature"> :boolean</span></h3><div class="description"><p>boolean dictating weather or not to do assembly ; supported by mcif, pdb</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="dontConnectDuplicatedAtoms"><span class="type-signature"></span>dontConnectDuplicatedAtoms<span class="type-signature"> :boolean</span></h3><div class="description"><p>do not detect bonds between symmetries generated with duplicateAssemblyAtoms (cif only - other formats never make bonds between symmetries)</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="duplicateAssemblyAtoms"><span class="type-signature"></span>duplicateAssemblyAtoms<span class="type-signature"> :boolean</span></h3><div class="description"><p>Set to true if you wish to duplicate assembly atoms otherwise false ; supported by all formats with symmetries. Not duplicating will result in faster rendering but it will not be possible to individually style symmetries.</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="frames"><span class="type-signature"></span>frames<span class="type-signature"> :boolean</span></h3><div class="description"><p>true if you want to add to a new frame and false otherwise ; supported by 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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="hbondCutoff"><span class="type-signature"></span>hbondCutoff<span class="type-signature"> :number</span></h3><div class="description"><p>maximum distance used for identifying hydrogen bonds when computing secondary structure; supported by pdb, mmtf, cif</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="keepH"><span class="type-signature"></span>keepH<span class="type-signature"> :boolean</span></h3><div class="description"><p>do not strip hydrogens ; supported by sdf,mol2</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="multimodel"><span class="type-signature"></span>multimodel<span class="type-signature"> :boolean</span></h3><div class="description"><p>specifies whether or not multiple models are being defined ; supported by xyz,sdf, or mol2</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="noComputeSecondaryStructure"><span class="type-signature"></span>noComputeSecondaryStructure<span class="type-signature"> :boolean</span></h3><div class="description"><p>do not compute ss ; supported by pdb, mmtf, cif</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="noSecondaryStructure"><span class="type-signature"></span>noSecondaryStructure<span class="type-signature"> :boolean</span></h3><div class="description"><p>boolean dictating the presence of a secondary structure ; supported by pdb</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="normalizeAssembly"><span class="type-signature"></span>normalizeAssembly<span class="type-signature"> :boolean</span></h3><div class="description"><p>shift symmetry mates so their centroid is in the unit cell</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="onemol"><span class="type-signature"></span>onemol<span class="type-signature"> :boolean</span></h3><div class="description"><p>specifies weather or not the model is of one molecule ; Supported by xyz , sdf , mol2</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="parseStyle"><span class="type-signature"></span>parseStyle<span class="type-signature"> :unknown</span></h3><div class="description"><p>used to define ChemDoodle styles ; supported by cdjson</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">unknown</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.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>set model to this style after parsing</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="unboundCations"><span class="type-signature"></span>unboundCations<span class="type-signature"> :boolean</span></h3><div class="description"><p>for formats without explicit bonds, if assigning bonds to not assign bonds to common cations</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="vibrate"><span class="type-signature"></span>vibrate<span class="type-signature"> :object</span></h3><div class="description"><p>object specifying the vibration behavior ; supported by all</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">object</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>Attributes</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>frames</code></td><td class="type"><span class="param-type">number</span></td><td class="attributes"><optional><br></td><td class="description last"><p>vibrate.frames - number of frames to be created, default to 10 ; supported by all</p></td></tr><tr><td class="name"><code>amplitude</code></td><td class="type"><span class="param-type">number</span></td><td class="attributes"><optional><br></td><td class="description last"><p>vibrate.amplitude -amplitude of distortion, default to 1 (full) ; supported by 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_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="wrapAtoms"><span class="type-signature"></span>wrapAtoms<span class="type-signature"> :boolean</span></h3><div class="description"><p>Set to true with duplicateAssemblyAtoms to individually wrap atoms (from symmetries) into unit cell</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="parsers_ParserOptionsSpec.ts.html">parsers/ParserOptionsSpec.ts</a></li></ul></dd></div></dl></article></section><footer class="footer" id="PeOAagUepe"><div class="wrapper">3Dmol.js © 2019-2024 | <a href="https://pitt.edu/" target="_blank">University of Pittsburgh</a> | <a href="https://github.com/3dmol/3Dmol.js/blob/master/LICENSE" target="_blank">License</a></div></footer></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 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