@ccp-nc/crystvis-js 0.6.1 → 0.7.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (64) hide show
  1. package/.mocharc.yml +4 -0
  2. package/.vscode/settings.json +5 -1
  3. package/CHANGELOG.md +54 -16
  4. package/README.md +75 -2
  5. package/audit.txt +12 -25
  6. package/changes.txt +1 -26
  7. package/demo/demo.css +15 -10
  8. package/demo/index.html +32 -5
  9. package/demo/main.js +149 -42
  10. package/lib/formats/magres.js +156 -1
  11. package/lib/model.js +31 -0
  12. package/lib/modelview.js +24 -0
  13. package/lib/render.js +97 -2
  14. package/lib/selbox.js +18 -4
  15. package/lib/visualizer.js +237 -1
  16. package/outdated.txt +9 -12
  17. package/package.json +7 -5
  18. package/test/data/hf_mu_test.magres +62 -0
  19. package/test/data/hf_test.magres +61 -0
  20. package/test/data/optimized_muon_65-hf.magres +1424 -0
  21. package/test/loader.js +115 -1
  22. package/test/model.js +118 -0
  23. package/test/setup-dom.cjs +147 -0
  24. package/test/visualizer.js +475 -0
  25. package/docs/data/search.json +0 -1
  26. package/docs/fonts/Inconsolata-Regular.ttf +0 -0
  27. package/docs/fonts/OpenSans-Regular.ttf +0 -0
  28. package/docs/fonts/WorkSans-Bold.ttf +0 -0
  29. package/docs/index.html +0 -10
  30. package/docs/lib_model.module_js-AtomImage.html +0 -3
  31. package/docs/lib_model.module_js-BondImage.html +0 -3
  32. package/docs/lib_model.module_js-Model.html +0 -3
  33. package/docs/lib_model.module_js.html +0 -3
  34. package/docs/lib_modelview.module_js-ModelView.html +0 -12
  35. package/docs/lib_modelview.module_js.html +0 -3
  36. package/docs/lib_visualizer.module_js-CrystVis.html +0 -3
  37. package/docs/lib_visualizer.module_js.html +0 -3
  38. package/docs/model.js.html +0 -2160
  39. package/docs/modelview.js.html +0 -449
  40. package/docs/scripts/core.js +0 -726
  41. package/docs/scripts/core.min.js +0 -23
  42. package/docs/scripts/resize.js +0 -90
  43. package/docs/scripts/search.js +0 -265
  44. package/docs/scripts/search.min.js +0 -6
  45. package/docs/scripts/third-party/Apache-License-2.0.txt +0 -202
  46. package/docs/scripts/third-party/fuse.js +0 -9
  47. package/docs/scripts/third-party/hljs-line-num-original.js +0 -369
  48. package/docs/scripts/third-party/hljs-line-num.js +0 -1
  49. package/docs/scripts/third-party/hljs-original.js +0 -5171
  50. package/docs/scripts/third-party/hljs.js +0 -1
  51. package/docs/scripts/third-party/popper.js +0 -5
  52. package/docs/scripts/third-party/tippy.js +0 -1
  53. package/docs/scripts/third-party/tocbot.js +0 -672
  54. package/docs/scripts/third-party/tocbot.min.js +0 -1
  55. package/docs/styles/clean-jsdoc-theme-base.css +0 -1159
  56. package/docs/styles/clean-jsdoc-theme-dark.css +0 -412
  57. package/docs/styles/clean-jsdoc-theme-light.css +0 -482
  58. package/docs/styles/clean-jsdoc-theme-scrollbar.css +0 -30
  59. package/docs/styles/clean-jsdoc-theme-without-scrollbar.min.css +0 -1
  60. package/docs/styles/clean-jsdoc-theme.min.css +0 -1
  61. package/docs/tutorial-Events.html +0 -13
  62. package/docs/tutorial-Queries.html +0 -16
  63. package/docs/tutorial-ThreejsMigration.html +0 -25
  64. package/docs/visualizer.js.html +0 -574
package/docs/lib_modelview.module_js-ModelView.html DELETED
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7h18v2H3v-2zm0 7h18v2H3v-2z"/></symbol></defs></svg></head><body data-theme="dark"><div class="sidebar-container"><div class="sidebar" id="sidebar"><div class="sidebar-items-container"><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-modules"><div>Modules</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="lib_model.module_js.html">lib/model.js</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js.html">lib/modelview.js</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js.html">lib/visualizer.js</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-classes"><div>Classes</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="lib_model.module_js-AtomImage.html">AtomImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-BondImage.html">BondImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-Model.html">Model</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js-ModelView.html">ModelView</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js-CrystVis.html">CrystVis</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-tutorials"><div>Tutorials</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="tutorial-Events.html">Events</a></div><div class="sidebar-section-children"><a href="tutorial-Queries.html">Queries</a></div><div class="sidebar-section-children"><a href="tutorial-ThreejsMigration.html">ThreejsMigration</a></div></div></div></div></div><div class="navbar-container" id="VuAckcnZhf"><nav class="navbar"><div class="navbar-left-items"></div><div class="navbar-right-items"><div class="navbar-right-item"><button class="icon-button search-button" aria-label="open-search"><svg><use xlink:href="#search-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button theme-toggle" aria-label="toggle-theme"><svg><use class="theme-svg-use" xlink:href="#light-theme-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button font-size" aria-label="change-font-size"><svg><use xlink:href="#font-size-icon"></use></svg></button></div></div><nav></nav></nav></div><div class="toc-container"><div class="toc-content"><span class="bold">On this page</span><div id="eed4d2a0bfd64539bb9df78095dec881"></div></div></div><div class="body-wrapper"><div class="main-content"><div class="main-wrapper"><section><header><h1 id="ModelView-title" class="has-anchor"><span class="ancestors"><a href="lib_modelview.module_js.html">lib/modelview.js</a>~</span> ModelView</h1><div class="class-description"><p>A 'view' representing a subset of atom images of a model, used for selection and further manipulations</p></div></header><article><div class="container-overview"><h2 id="constructor" class="has-anchor">Constructor</h2><h3 class="name has-anchor" id="ModelView"><span class="type-signature"></span>new ModelView<span class="signature">(model, indices)</span></h3><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>model</code></td><td class="type"><span class="param-type">Model</span></td><td class="description last"><p>Model to use for the view</p></td></tr><tr><td class="name"><code>indices</code></td><td class="type"><span class="param-type">Array.&lt;int></span></td><td class="description last"><p>Indices of the atom images to include in the view</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line12">line 12</a></li></ul></dd></div></dl></div><h2 id="members" class="subsection-title has-anchor">Members</h2><h3 class="name has-anchor" id="atoms"><span class="type-signature">(readonly) </span>atoms<span class="type-signature"> :Array.&lt;AtomImage></span></h3><div class="description"><p>Atom images in this view</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 bold">Source</dt><dd class="tag-source"><ul><li><a href="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line62">line 62</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="elements"><span class="type-signature"></span>elements<span class="type-signature"></span></h3><div class="description"><p>Get sorted set of unique elements in the ModelView</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line284">line 284</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="indices"><span class="type-signature">(readonly) </span>indices<span class="type-signature"> :Array.&lt;int></span></h3><div class="description"><p>Indices of the atom images in this view</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 bold">Source</dt><dd class="tag-source"><ul><li><a href="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line53">line 53</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="length"><span class="type-signature">(readonly) </span>length<span class="type-signature"> :int</span></h3><div class="description"><p>Number of atom images in this view</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">int</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line71">line 71</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="model"><span class="type-signature">(readonly) </span>model<span class="type-signature"> :Model</span></h3><div class="description"><p>Model used by this view</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Model</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line44">line 44</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="unique_labels_multiplicity"><span class="type-signature">(readonly) </span>unique_labels_multiplicity<span class="type-signature"> :Object.&lt;string, int></span></h3><div class="description"><p>Multiplicity of the atoms in the view</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Object.&lt;string, int></span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line82">line 82</a></li></ul></dd></div></dl><h2 id="methods" class="subsection-title has-anchor">Methods</h2><h3 class="name has-anchor" id="addEllipsoids"><span class="type-signature"></span>addEllipsoids<span class="signature">(data, name, args)</span></h3><div class="description"><p>Add ellipsoids to the atom images in this ModelView</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>data</code></td><td class="type"><span class="param-type">Object</span> |<wbr> <span class="param-type">Array.&lt;Object></span> |<wbr> <span class="param-type">function</span></td><td class="default"></td><td class="description last"><p>Data to use for the ellipsoid (see AtomImage.addEllipsoid for details)</p></td></tr><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span> |<wbr> <span class="param-type">Array.&lt;String></span> |<wbr> <span class="param-type">function</span></td><td class="default">ellipsoid</td><td class="description last"><p>Name of the ellipsoids</p></td></tr><tr><td class="name"><code>args</code></td><td class="type"><span class="param-type">Object</span> |<wbr> <span class="param-type">Array.&lt;Object></span> |<wbr> <span class="param-type">function</span></td><td class="default"></td><td class="description last"><p>Arguments for creating the ellipsoids</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line378">line 378</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="addLabels"><span class="type-signature"></span>addLabels<span class="signature">(text, name, args)</span></h3><div class="description"><p>Add labels to the atom images in this ModelView</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>text</code></td><td class="type"><span class="param-type">String</span> |<wbr> <span class="param-type">Array.&lt;String></span> |<wbr> <span class="param-type">function</span></td><td class="default"></td><td class="description last"><p>Text of the labels, as single value, array, or function returning a string for each atom image.</p></td></tr><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span> |<wbr> <span class="param-type">Array.&lt;String></span> |<wbr> <span class="param-type">function</span></td><td class="default">label</td><td class="description last"><p>Name of the label</p></td></tr><tr><td class="name"><code>args</code></td><td class="type"><span class="param-type">Object</span> |<wbr> <span class="param-type">Array.&lt;Object></span> |<wbr> <span class="param-type">function</span></td><td class="default"></td><td class="description last"><p>Arguments for creating the label</p></td></tr></tbody></table></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line298">line 298</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="and"><span class="type-signature"></span>and<span class="signature">(mview)</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Intersection with another ModelView</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>mview</code></td><td class="type"><span class="param-type">ModelView</span></td><td class="description last"><p>Other view</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line162">line 162</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Result</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">ModelView</span></dd></dl></div><h3 class="name has-anchor" id="ellipsoidProperties"><span class="type-signature"></span>ellipsoidProperties<span class="signature">(name, property, value)</span></h3><div class="description"><p>Get or set ellipsoids' properties for the atom images in this ModelView</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span> |<wbr> <span class="param-type">Array.&lt;String></span> |<wbr> <span class="param-type">function</span></td><td class="default">ellipsoid</td><td class="description last"><p>Name of the ellipsoids</p></td></tr><tr><td class="name"><code>property</code></td><td class="type"><span class="param-type">String</span> |<wbr> <span class="param-type">Array.&lt;String></span> |<wbr> <span class="param-type">function</span></td><td class="default">color</td><td class="description last"><p>Property to get or set</p></td></tr><tr><td class="name"><code>value</code></td><td class="type"><span class="param-type">Any</span> |<wbr> <span class="param-type">Array.&lt;Any></span> |<wbr> <span class="param-type">function</span></td><td class="default">null</td><td class="description last"><p>If not provided, get. If provided, set this value</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line417">line 417</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="find"><span class="type-signature"></span>find<span class="signature">(query)</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Perform a further search within the atoms included in this ModelView.</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>query</code></td><td class="type"><span class="param-type">Array</span></td><td class="description last"><p>Query for the search, formatted as for the Model.find function.</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line150">line 150</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Result of the query</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">ModelView</span></dd></dl></div><h3 class="name has-anchor" id="hide"><span class="type-signature"></span>hide<span class="signature">()</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Make all atoms in the view invisible. Can be chained</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line121">line 121</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">ModelView</span></dd></dl></div><h3 class="name has-anchor" id="labelProperties"><span class="type-signature"></span>labelProperties<span class="signature">(name, property, value)</span></h3><div class="description"><p>Get or set labels' properties for the atom images in this ModelView</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span> |<wbr> <span class="param-type">Array.&lt;String></span> |<wbr> <span class="param-type">function</span></td><td class="default">label</td><td class="description last"><p>Name of the labels</p></td></tr><tr><td class="name"><code>property</code></td><td class="type"><span class="param-type">String</span> |<wbr> <span class="param-type">Array.&lt;String></span> |<wbr> <span class="param-type">function</span></td><td class="default">color</td><td class="description last"><p>Property to get or set</p></td></tr><tr><td class="name"><code>value</code></td><td class="type"><span class="param-type">Any</span> |<wbr> <span class="param-type">Array.&lt;Any></span> |<wbr> <span class="param-type">function</span></td><td class="default">null</td><td class="description last"><p>If not provided, get. If provided, set this value</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line344">line 344</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="map"><span class="type-signature"></span>map<span class="signature">(func)</span><span class="type-signature"> &rarr; {Array}</span></h3><div class="description"><p>Run a function on each AtomImage, returning an Array of the results.</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>func</code></td><td class="type"><span class="param-type">function</span></td><td class="description last"><p>Function to run, should take AtomImage and index as arguments</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line134">line 134</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Return values</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">Array</span></dd></dl></div><h3 class="name has-anchor" id="not"><span class="type-signature"></span>not<span class="signature">()</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Complement to this ModelView</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line197">line 197</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Result</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">ModelView</span></dd></dl></div><h3 class="name has-anchor" id="or"><span class="type-signature"></span>or<span class="signature">(mview)</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Union with another ModelView</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>mview</code></td><td class="type"><span class="param-type">ModelView</span></td><td class="description last"><p>Other view</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line174">line 174</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Result</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">ModelView</span></dd></dl></div><h3 class="name has-anchor" id="remove"><span class="type-signature"></span>remove<span class="signature">()</span></h3><div class="description"><p>Remove all atoms in mview from the current view</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line205">line 205</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="removeEllipsoids"><span class="type-signature"></span>removeEllipsoids<span class="signature">(name)</span></h3><div class="description"><p>Remove ellipsoids from the atom images in this ModelView</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span> |<wbr> <span class="param-type">Array.&lt;String></span> |<wbr> <span class="param-type">function</span></td><td class="default">ellipsoid</td><td class="description last"><p>Name of the ellipsoids to remove</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line397">line 397</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="removeLabels"><span class="type-signature"></span>removeLabels<span class="signature">(name)</span></h3><div class="description"><p>Remove labels from the atom images in this ModelView</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span> |<wbr> <span class="param-type">Array.&lt;String></span> |<wbr> <span class="param-type">function</span></td><td class="default">label</td><td class="description last"><p>Name of the labels to remove</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line324">line 324</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="setProperty"><span class="type-signature"></span>setProperty<span class="signature">(name, value)</span></h3><div class="description"><p>Set some property of the atoms within the ModelView.</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="default"></td><td class="description last"><p>Name of the property to set</p></td></tr><tr><td class="name"><code>value</code></td><td class="type"><span class="param-type">int</span> |<wbr> <span class="param-type">Array</span> |<wbr> <span class="param-type">function</span></td><td class="default">null</td><td class="description last"><p>Value to set for the atoms. It can be either:</p><pre><code> 1. a single value for all of them
4
- 2. an Array of values as long as
5
- the ModelView
6
- 3. a function that accepts an
7
- AtomImage and an index and returns
8
- a value
9
-
10
- If left empty, the property is
11
- restored to its default value.
12
- </code></pre></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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line263">line 263</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="show"><span class="type-signature"></span>show<span class="signature">()</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Make all atoms in the view visible. Can be chained</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line112">line 112</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">ModelView</span></dd></dl></div><h3 class="name has-anchor" id="uniqueSites"><span class="type-signature"></span>uniqueSites<span class="signature">()</span></h3><div class="description"><p>Unique atoms in the current view (based on site labels)</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line215">line 215</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="xor"><span class="type-signature"></span>xor<span class="signature">(mview)</span><span class="type-signature"> &rarr; {ModelView}</span></h3><div class="description"><p>Exclusive OR with another ModelView</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>mview</code></td><td class="type"><span class="param-type">ModelView</span></td><td class="description last"><p>Other view</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line186">line 186</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Result</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">ModelView</span></dd></dl></div></article></section></div></div></div><div class="search-container" id="PkfLWpAbet" style="display:none"><div class="wrapper" id="iCxFxjkHbP"><button class="icon-button search-close-button" id="VjLlGakifb" aria-label="close search"><svg><use xlink:href="#close-icon"></use></svg></button><div class="search-box-c"><svg><use xlink:href="#search-icon"></use></svg> <input type="text" id="vpcKVYIppa" class="search-input" placeholder="Search..." autofocus></div><div class="search-result-c" id="fWwVHRuDuN"><span class="search-result-c-text">Type anything to view search result</span></div></div></div><div class="mobile-menu-icon-container"><button class="icon-button" id="mobile-menu" data-isopen="false" aria-label="menu"><svg><use xlink:href="#menu-icon"></use></svg></button></div><div id="mobile-sidebar" class="mobile-sidebar-container"><div class="mobile-sidebar-wrapper"><div class="mobile-nav-links"></div><div class="mobile-sidebar-items-c"><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-modules"><div>Modules</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="lib_model.module_js.html">lib/model.js</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js.html">lib/modelview.js</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js.html">lib/visualizer.js</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-classes"><div>Classes</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="lib_model.module_js-AtomImage.html">AtomImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-BondImage.html">BondImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-Model.html">Model</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js-ModelView.html">ModelView</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js-CrystVis.html">CrystVis</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-tutorials"><div>Tutorials</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="tutorial-Events.html">Events</a></div><div class="sidebar-section-children"><a href="tutorial-Queries.html">Queries</a></div><div class="sidebar-section-children"><a href="tutorial-ThreejsMigration.html">ThreejsMigration</a></div></div></div><div class="mobile-navbar-actions"><div class="navbar-right-item"><button class="icon-button search-button" aria-label="open-search"><svg><use xlink:href="#search-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button theme-toggle" aria-label="toggle-theme"><svg><use class="theme-svg-use" xlink:href="#light-theme-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button font-size" aria-label="change-font-size"><svg><use xlink:href="#font-size-icon"></use></svg></button></div></div></div></div><script type="text/javascript" src="scripts/core.min.js"></script><script src="scripts/search.min.js" defer="defer"></script><script src="scripts/third-party/fuse.js" defer="defer"></script><script type="text/javascript">var tocbotInstance=tocbot.init({tocSelector:"#eed4d2a0bfd64539bb9df78095dec881",contentSelector:".main-content",headingSelector:"h1, h2, h3",hasInnerContainers:!0,scrollContainer:".main-content",headingsOffset:130,onClick:bringLinkToView})</script></body></html>
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class="description"><p>Class holding &quot;model views&quot;, subsets of atoms in a Model used for selection or to perform operations in block</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="modelview.js.html">modelview.js</a>, <a href="modelview.js.html#line3">line 3</a></li></ul></dd></div></dl></div><h2 id="classes" class="subsection-title has-anchor">Classes</h2><dl><dt><a href="lib_modelview.module_js-ModelView.html">ModelView</a></dt><dd></dd></dl></article></section></div></div></div><div class="search-container" id="PkfLWpAbet" style="display:none"><div class="wrapper" id="iCxFxjkHbP"><button class="icon-button search-close-button" id="VjLlGakifb" aria-label="close search"><svg><use xlink:href="#close-icon"></use></svg></button><div class="search-box-c"><svg><use xlink:href="#search-icon"></use></svg> <input type="text" id="vpcKVYIppa" class="search-input" placeholder="Search..." 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href="lib_model.module_js-AtomImage.html">AtomImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-BondImage.html">BondImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-Model.html">Model</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js-ModelView.html">ModelView</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js-CrystVis.html">CrystVis</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-tutorials"><div>Tutorials</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="tutorial-Events.html">Events</a></div><div class="sidebar-section-children"><a href="tutorial-Queries.html">Queries</a></div><div class="sidebar-section-children"><a href="tutorial-ThreejsMigration.html">ThreejsMigration</a></div></div></div></div></div><div class="navbar-container" id="VuAckcnZhf"><nav class="navbar"><div class="navbar-left-items"></div><div class="navbar-right-items"><div class="navbar-right-item"><button class="icon-button search-button" aria-label="open-search"><svg><use xlink:href="#search-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button theme-toggle" aria-label="toggle-theme"><svg><use class="theme-svg-use" xlink:href="#light-theme-icon"></use></svg></button></div><div class="navbar-right-item"><button class="icon-button font-size" aria-label="change-font-size"><svg><use xlink:href="#font-size-icon"></use></svg></button></div></div><nav></nav></nav></div><div class="toc-container"><div class="toc-content"><span class="bold">On this page</span><div id="eed4d2a0bfd64539bb9df78095dec881"></div></div></div><div class="body-wrapper"><div class="main-content"><div class="main-wrapper"><section><header><h1 id="CrystVis-title" class="has-anchor"><span class="ancestors"><a href="lib_visualizer.module_js.html">lib/visualizer.js</a>~</span> CrystVis</h1><div class="class-description"><p>An object providing a full interface to a renderer for crystallographic models</p></div></header><article><div class="container-overview"><h2 id="constructor" class="has-anchor">Constructor</h2><h3 class="name has-anchor" id="CrystVis"><span class="type-signature"></span>new CrystVis<span class="signature">(element, width, height, rendererOptions)</span></h3><div class="description"><p>An object providing a full interface to a renderer for crystallographic models</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>element</code></td><td class="type"><span class="param-type">string</span></td><td class="default"></td><td class="description last"><p>CSS-style identifier for the HTML element to put the renderer in</p></td></tr><tr><td class="name"><code>width</code></td><td class="type"><span class="param-type">int</span></td><td class="default">0</td><td class="description last"><p>Window width</p></td></tr><tr><td class="name"><code>height</code></td><td class="type"><span class="param-type">int</span></td><td class="default">0</td><td class="description last"><p>Window height. If both this and width are set to 0, the window fits its context and automatically resizes with it</p></td></tr><tr><td class="name"><code>rendererOptions</code></td><td class="type"><span class="param-type">Object</span></td><td class="default"></td><td class="description last"><p>Options for the renderer</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line38">line 38</a></li></ul></dd></div></dl></div><h2 id="members" class="subsection-title has-anchor">Members</h2><h3 class="name has-anchor" id="displayed"><span class="type-signature"></span>displayed<span class="type-signature"> :ModelView</span></h3><div class="description"><p>Displayed atoms</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">ModelView</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line121">line 121</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="highlightSelected"><span class="type-signature"></span>highlightSelected<span class="type-signature"> :bool</span></h3><div class="description"><p>Whether the selected atoms should be highlighted with auras</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">bool</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line154">line 154</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="model"><span class="type-signature">(readonly) </span>model<span class="type-signature"> :Model</span></h3><div class="description"><p>Currently loaded model</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">Model</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line104">line 104</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="modelList"><span class="type-signature">(readonly) </span>modelList<span class="type-signature"> :Array</span></h3><div class="description"><p>List of loaded models</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line95">line 95</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="modelName"><span class="type-signature">(readonly) </span>modelName<span class="type-signature"> :String</span></h3><div class="description"><p>Name of the currently loaded model</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line113">line 113</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="selected"><span class="type-signature"></span>selected<span class="type-signature"> :ModelView</span></h3><div class="description"><p>Selected atoms</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">ModelView</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line138">line 138</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="theme"><span class="type-signature"></span>theme<span class="type-signature"> :object</span></h3><div class="description"><p>Theme</p></div><div class="member-item-container flex"><strong>Type:</strong><ul><li><span class="param-type">object</span></li></ul></div><dl class="details"><div class="details-item-container"><dt class="tag-source bold">Source</dt><dd class="tag-source"><ul><li><a href="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line177">line 177</a></li></ul></dd></div></dl><h2 id="methods" class="subsection-title has-anchor">Methods</h2><h3 class="name has-anchor" id="addNotification"><span class="type-signature"></span>addNotification<span class="signature">()</span></h3><div class="description"><p>Add a notification to the list of notifications to be displayed</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line508">line 508</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="addNotifications"><span class="type-signature"></span>addNotifications<span class="signature">()</span></h3><div class="description"><p>Adds all notifications to the drawing</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line517">line 517</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="addPrimitive"><span class="type-signature"></span>addPrimitive<span class="signature">(p)</span></h3><div class="description"><p>Add a primitive shape to the drawing</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>p</code></td><td class="type"><span class="param-type">THREE.<wbr>Object3D</span></td><td class="description last"><p>Primitive to add</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line492">line 492</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="centerCamera"><span class="type-signature"></span>centerCamera<span class="signature">(center, shift)</span></h3><div class="description"><p>Center the camera on a given point</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>center</code></td><td class="type"><span class="param-type">Array.&lt;float></span></td><td class="description last"><p>Point in model space that the orbiting camera should be centred on and look at</p></td></tr><tr><td class="name"><code>shift</code></td><td class="type"><span class="param-type">Array.&lt;float></span></td><td class="description last"><p>Shift (in units of width/height of the canvas) with which the center of the camera should be rendered with respect to the center of the canvas</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line318">line 318</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="clearNotifications"><span class="type-signature"></span>clearNotifications<span class="signature">()</span></h3><div class="description"><p>Removes notifications from the drawing</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line528">line 528</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="deleteModel"><span class="type-signature"></span>deleteModel<span class="signature">(name)</span></h3><div class="description"><p>Erase a model from the recorded ones</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="description last"><p>Name of the model to delete</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line474">line 474</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="displayModel"><span class="type-signature"></span>displayModel<span class="signature">(name)</span></h3><div class="description"><p>Render a 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>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="default">null</td><td class="description last"><p>Name of the model to display. If empty, just clear the renderer window.</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line424">line 424</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="getScreenshotData"><span class="type-signature"></span>getScreenshotData<span class="signature">()</span><span class="type-signature"> &rarr; {String}</span></h3><div class="description"><p>Recover a data URL of a PNG screenshot of the current scene</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line538">line 538</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>A data URL of the PNG screenshot</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">String</span></dd></dl></div><h3 class="name has-anchor" id="loadModels"><span class="type-signature"></span>loadModels<span class="signature">(contents, format, prefix, parameters)</span><span class="type-signature"> &rarr; {Object}</span></h3><div class="description"><p>Load one or more atomic models from a file's contents</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>contents</code></td><td class="type"><span class="param-type">String</span></td><td class="default"></td><td class="description last"><p>The contents of the structure file</p></td></tr><tr><td class="name"><code>format</code></td><td class="type"><span class="param-type">String</span></td><td class="default">cif</td><td class="description last"><p>The file's format (cif, xyz, etc.). Default is cif.</p></td></tr><tr><td class="name"><code>prefix</code></td><td class="type"><span class="param-type">String</span></td><td class="default">null</td><td class="description last"><p>Prefix to use when naming the models. Default is empty.</p></td></tr><tr><td class="name"><code>parameters</code></td><td class="type"><span class="param-type">Object</span></td><td class="default"></td><td class="description last"><p>Loading parameters:</p><ul><li><code>supercell</code>: supercell size (only used if the structure is periodic)</li><li><code>molecularCrystal</code>: if true, try to make the model load completing molecules across periodic boundaries</li><li><code>useNMRActiveIsotopes</code>: if true, all isotopes are set by default to the most common one with non-zero spin</li><li><code>vdwScaling</code>: scale van der Waals radii by a constant factor</li><li><code>vdwElementScaling</code>: table of per-element factors to scale VdW radii by</li></ul></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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line341">line 341</a></li></ul></dd></div></dl><div class="method-member-container mt-20"><strong>Returns:</strong><div class="param-desc"><p>Names of the models we tried to load, and values of true/false for successful loading or not</p></div><dl class="param-type"><dt>Type:&nbsp;</dt><dd><span class="param-type">Object</span></dd></dl></div><h3 class="name has-anchor" id="onAtomBox"><span class="type-signature"></span>onAtomBox<span class="signature">(callback)</span></h3><div class="description"><p>Set a callback function for an event where a user drags a box around multiple atoms. The function should take as arguments a ModelView including the atoms in the box:</p><p>function callback(view) { ... }</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>callback</code></td><td class="type"><span class="param-type">function</span></td><td class="default">null</td><td class="description last"><p>Callback function for the event. Passing &quot;null&quot; restores default behaviour</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line249">line 249</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="onAtomClick"><span class="type-signature"></span>onAtomClick<span class="signature">(callback, modifiers)</span></h3><div class="description"><p>Set a callback function for an event where a user clicks on an atom. The function should take as arguments the atom image for the clicked atom and the event object:</p><p>function callback(atom, event) { ... }</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th>Default</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>callback</code></td><td class="type"><span class="param-type">function</span></td><td class="default">null</td><td class="description last"><p>Callback function for the event. Passing &quot;null&quot; restores default behaviour</p></td></tr><tr><td class="name"><code>modifiers</code></td><td class="type"><span class="param-type">int</span></td><td class="default"></td><td class="description last"><p>Click event. Use the following flags to define it:</p><ul><li>CrystVis.LEFT_CLICK</li><li>CrystVis.RIGHT_CLICK</li><li>CrystVis.MIDDLE_CLICK</li><li>CrystVis.CTRL_BUTTON</li><li>CrystVis.ALT_BUTTON</li><li>CrystVis.SHIFT_BUTTON</li><li>CrystVis.CMD_BUTTON</li></ul><p>For example, CrystVis.LEFT_CLICK + CrystVis.SHIFT_BUTTON defines the event for a click while the Shift key is pressed.</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line219">line 219</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="reloadModel"><span class="type-signature"></span>reloadModel<span class="signature">(name, parameters)</span></h3><div class="description"><p>Reload a model, possibly with new parameters</p></div><div class="method-member-container flex flex-col w-100 overflow-auto mt-20"><strong>Parameters:</strong><table class="params"><thead><tr><th>Name</th><th>Type</th><th class="last">Description</th></tr></thead><tbody><tr><td class="name"><code>name</code></td><td class="type"><span class="param-type">String</span></td><td class="description last"><p>Name of the model to reload.</p></td></tr><tr><td class="name"><code>parameters</code></td><td class="type"><span class="param-type">Object</span></td><td class="description last"><p>Loading parameters as in .loadModels()</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line394">line 394</a></li></ul></dd></div></dl><h3 class="name has-anchor" id="removePrimitive"><span class="type-signature"></span>removePrimitive<span class="signature">(p)</span></h3><div class="description"><p>Remove a primitive shape from the drawing</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>p</code></td><td class="type"><span class="param-type">THREE.<wbr>Object3D</span></td><td class="description last"><p>Primitive to remove</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="visualizer.js.html">visualizer.js</a>, <a href="visualizer.js.html#line501">line 501</a></li></ul></dd></div></dl></article></section></div></div></div><div class="search-container" id="PkfLWpAbet" style="display:none"><div class="wrapper" id="iCxFxjkHbP"><button class="icon-button search-close-button" id="VjLlGakifb" aria-label="close search"><svg><use xlink:href="#close-icon"></use></svg></button><div class="search-box-c"><svg><use xlink:href="#search-icon"></use></svg> <input 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