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KekuleJS

Implementation of KekuleJS in LiaScript

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Install / Use

/learn @LiaTemplates/KekuleJS
About this skill

Quality Score

0/100

Supported Platforms

Universal

README

<!-- author: Yannik Höll email: labruzzler@gmail.com version: 0.0.2 language: en narrator: US English Female script: http://cdnjs.cloudflare.com/ajax/libs/raphael/2.1.0/raphael-min.js https://cdn.jsdelivr.net/gh/LiaTemplates/KekuleJS/kekule/three.js https://cdn.jsdelivr.net/gh/LiaTemplates/KekuleJS/kekule/kekule.min.js link: https://cdn.jsdelivr.net/gh/LiaTemplates/KekuleJS/kekule/themes/default/kekule.css @Kekule.molecule2d: @Kekule._load2d(@uid,cml,@0) @Kekule.load2d: @Kekule._load2d(@uid,@0,@1) @Kekule.eval2d: @Kekule._load2d(@uid,@0,`@input`) @Kekule._load2d <script> let rem = document.getElementsByClassName("deleteme") for( let i=0; i< rem.length; i++ ) rem[i].innerHTML = "" const div = document.getElementById("molecule_parent1_@0"); const rawData = `@2`; const mol = Kekule.IO.loadFormatData(rawData, '@1'); var viewer = new Kekule.ChemWidget.Viewer2D(document, mol); viewer.removeClassName(Kekule.Widget.HtmlClassNames.NORMAL_BACKGROUND); div.appendChild(viewer.getElement()); "LIA: stop" </script> <div style="text-align: center" id="molecule_parent1_@0" class="deleteme"></div> @end @Kekule.molecule3d: @Kekule._load3d(@uid,cml,@0) @Kekule.eval3d: @Kekule._load3d(@uid,@0,`@input`) @Kekule.load3d: @Kekule._load3d(@uid,@0,@1) @Kekule._load3d <script> let rem = document.getElementsByClassName("deleteme") for( let i=0; i< rem.length; i++ ) rem[i].innerHTML = ""; const div = document.getElementById("molecule_parent2_@0"); const rawData = `@2`; let mol = Kekule.IO.loadFormatData(rawData, '@1'); var viewer = new Kekule.ChemWidget.Viewer(div); viewer.setChemObj(mol); viewer.setZoom(1.5); viewer.setRenderType(Kekule.Render.RendererType.R3D); viewer.setAutofit(true); viewer.setEnableToolbar(true); "LIA: stop" </script> <div data-widget="Kekule.ChemWidget.Viewer" style="width: 100%; height: 550px;" id="molecule_parent2_@0" class="deleteme"></div> @end @Kekule.periodicTable: @_periodicTable_(@0, @uid) @_periodicTable_ <div style="text-align: center" id="periodic_table_@1" class="deleteme"></div> <script> let rem = document.getElementsByClassName("deleteme") for( let i=0; i< rem.length; i++ ) rem[i].innerHTML = ""; const div = document.getElementById("periodic_table_@1"); const periodic_table = new Kekule.ChemWidget.PeriodicTable(document); if("@0" !== "large") periodic_table.useMiniMode = true; else periodic_table.useMiniMode = false; periodic_table.setEnableSelect(true) .setDisplayedComponents(['symbol', 'name', 'atomicNumber']) .appendToElem(div); console.log("plotting: ", `@0`) </script> @end @Kekule.load: @Kekule.load_(@uid,@0) @Kekule.load_ <div id="structureContainer_@0"></div> <script> // Load the XYZ file from a URL Kekule.IO.loadUrlData('@1', (mol, success) => { if (!success) { document.getElementById("structureContainer_@0").innerHTML = 'Failed to load @1'; return; } var viewer = new Kekule.ChemWidget.Viewer(document); viewer.setDimension('100%', '60vh'); viewer.appendToElem(document.getElementById('structureContainer_@0')).setChemObj(mol); viewer.setAutofit(true); viewer.setEnableToolbar(true); viewer.setRenderType(Kekule.Render.RendererType.R3D); }); console.log("loading file", Kekule) </script> @end -->

Kekelu JS

Implementation of the the JS library KekuleJS which provides tool for rendering molecules and much more chemical notation.

KekuleJS Source <br> LiaScript Page

@Kekule.molecule2d

Put the cml representation of the molecule you want to render into markdown quotes and put the macro @Kekule.molecule2d on the first line of the markdown block.

<p style="color: red">You have to be carful that your cml code does not contain any `@`-Symbols or the macro will not work. (Sometimes these symbols are in the meta info.)</p> 
<cml xmlns="http://www.xml-cml.org/schema">
  <molecule>
    <atomArray>
      <atom id="a1588768090561" elementType="C" x2="0.4125" y2="0.6348"/>
      <atom id="a1588768090562" elementType="C" x2="-0.4125" y2="0.6348"/>
      <atom id="a1588768090563" elementType="C" x2="-0.6674" y2="-0.1498"/>
      <atom id="a1588768090564" elementType="N" x2="0" y2="-0.6348"/>
      <atom id="a1588768090565" elementType="C" x2="0.6674" y2="-0.1498"/>
    </atomArray>
    <bondArray>
      <bond id="b1588768090566" order="S" atomRefs2="a1588768090561 a1588768090562"/>
      <bond id="b1588768090567" order="D" atomRefs2="a1588768090562 a1588768090563"/>
      <bond id="b1588768090568" order="S" atomRefs2="a1588768090563 a1588768090564"/>
      <bond id="b1588768090569" order="S" atomRefs2="a1588768090564 a1588768090565"/>
      <bond id="b1588768090570" order="D" atomRefs2="a1588768090565 a1588768090561"/>
    </bondArray>
  </molecule>
</cml>

The code above gets interpreted as this molecule:

<cml xmlns="http://www.xml-cml.org/schema">
  <molecule>
    <atomArray>
      <atom id="a1588768090561" elementType="C" x2="0.4125" y2="0.6348"/>
      <atom id="a1588768090562" elementType="C" x2="-0.4125" y2="0.6348"/>
      <atom id="a1588768090563" elementType="C" x2="-0.6674" y2="-0.1498"/>
      <atom id="a1588768090564" elementType="N" x2="0" y2="-0.6348"/>
      <atom id="a1588768090565" elementType="C" x2="0.6674" y2="-0.1498"/>
    </atomArray>
    <bondArray>
      <bond id="b1588768090566" order="S" atomRefs2="a1588768090561 a1588768090562"/>
      <bond id="b1588768090567" order="D" atomRefs2="a1588768090562 a1588768090563"/>
      <bond id="b1588768090568" order="S" atomRefs2="a1588768090563 a1588768090564"/>
      <bond id="b1588768090569" order="S" atomRefs2="a1588768090564 a1588768090565"/>
      <bond id="b1588768090570" order="D" atomRefs2="a1588768090565 a1588768090561"/>
    </bondArray>
  </molecule>
</cml>

@Kekule.molecule3d

Put the cml representation of the molecule you want to render into markdown quotes and put the macro @Kekule.molecule3d on the first line of the markdown block.

<p style="color: red">You have to be carful that your cml code does not contain any `@`-Symbols or the macro will not work. (Sometimes these symbols are in the meta info.)</p> 
<cml xmlns="http://www.xml-cml.org/schema">
  <molecule id="m1">
    <atomArray>
      <atom id="a4" elementType="C" x2="13.1708" y2="37.8126"/>
      <atom id="a11" elementType="N" x2="12.3867" y2="37.557500000000005"/>
      <atom id="a5" elementType="C" x2="13.1708" y2="38.637600000000006"/>
      <atom id="a3" elementType="N" x2="13.8865" y2="37.3986"/>
      <atom id="a14" elementType="C" x2="12.3867" y2="35.91630000000001"/>
      <atom id="a7" elementType="C" x2="11.9012" y2="38.225"/>
      <atom id="a6" elementType="C" x2="13.8865" y2="39.050000000000004"/>
      <atom id="a8" elementType="N" x2="12.3867" y2="38.8926"/>
      <atom id="a2" elementType="C" x2="14.6007" y2="37.8126"/>
      <atom id="a15" elementType="O" x2="11.270199999999999" y2="36.330200000000005"/>
      <atom id="a13" elementType="C" x2="11.9655" y2="35.432300000000005"/>
      <atom id="a21" elementType="H" x2="12.3867" y2="35.2079"/>
      <atom id="a1" elementType="N" x2="14.6007" y2="38.637600000000006"/>
      <atom id="a9" elementType="O" x2="13.8865" y2="39.875"/>
      <atom id="a10" elementType="N" x2="15.3178" y2="37.3986"/>
      <atom id="a16" elementType="C" x2="10.1478" y2="35.91630000000001"/>
      <atom id="a12" elementType="C" x2="10.5778" y2="35.432300000000005"/>
      <atom id="a19" elementType="H" x2="11.9655" y2="35.858000000000004"/>
      <atom id="a17" elementType="H" x2="11.9655" y2="34.88720000000001"/>
      <atom id="a22" elementType="C" x2="10.1478" y2="36.578"/>
      <atom id="a23" elementType="H" x2="10.1478" y2="35.2079"/>
      <atom id="a18" elementType="O" x2="10.5778" y2="34.88720000000001"/>
      <atom id="a20" elementType="H" x2="10.5778" y2="35.858000000000004"/>
      <atom id="a24" elementType="O" x2="9.4322" y2="36.9919"/>
    </atomArray>
    <bondArray>
      <bond id="b25" order="S" atomRefs2="a4 a11"/>
      <bond id="b4" order="D" atomRefs2="a4 a5"/>
      <bond id="b3" order="S" atomRefs2="a4 a3"/>
      <bond id="b23" order="S" atomRefs2="a11 a14"/>
      <bond id="b26" order="S" atomRefs2="a11 a7"/>
      <bond id="b5" order="S" atomRefs2="a5 a6"/>
      <bond id="b8" order="S" atomRefs2="a5 a8"/>
      <bond id="b2" order="D" atomRefs2="a3 a2"/>
      <bond id="b13" order="S" atomRefs2="a14 a15"/>
      <bond id="b12" order="S" atomRefs2="a14 a13"/>
      <bond id="b20" order="S" atomRefs2="a14 a21"/>
      <bond id="b7" order="D" atomRefs2="a7 a8"/>
      <bond id="b6" order="S" atomRefs2="a6 a1"/>
      <bond id="b9" order="D" atomRefs2="a6 a9"/>
      <bond id="b1" order="S" atomRefs2="a2 a1"/>
      <bond id="b10" order="S" atomRefs2="a2 a10"/>
      <bond id="b14" order="S" atomRefs2="a15 a16"/>
      <bond id="b11" order="S" atomRefs2="a13 a12"/>
      <bond id="b18" order="S" atomRefs2="a13 a19"/>
      <bond id="b16" order="S" atomRefs2="a13 a17"/>
      <bond id="b15" order="S" atomRefs2="a16 a12"/>
      <bond id="b21" order="S" atomRefs2="a16 a22"/>
      <bond id="b22" order="S" atomRefs2="a16 a23"/>
      <bond id="b17" order="S" atomRefs2="a12 a18"/>
      <bond id="b19" order="S" atomRefs2="a12 a20"/>
      <bond id="b24" order="S" atomRefs2="a22 a24"/>
    </bondArray>
  </molecule>
</cml>

The code above gets interpreted as this molecule:

<cml xmlns="http://www.xml-cml.org/schema">
  <molecule id="m1">
    <atomArray>
      <atom id="a4" elementType="C" x

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LiaTemplates

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GitHub Stars4
CategoryDevelopment
Updated5mo ago
Forks0
LiaTemplates/KekuleJS

Languages

JavaScript

Security Score

87/100

Audited on Nov 1, 2025

No findings