How to move from Marvin JS or Ketcher to Athanor

Marvin JS reaches end of sale on December 31, 2026 and end of life in December 2027. A page built on it can move to the Athanor editor by changing one script tag.

The one-line change

Before:

<script src="marvinjs/gui/lib/promise-1.0.0.min.js"></script>
<script src="marvinjs/js/marvinjslauncher.js"></script>
<iframe id="sketch" src="marvinjs/editor.html" style="width: 600px; height: 450px"></iframe>

After:

<script src="https://athanor.arbastro.com/app/embed/athanor-marvin.js"></script>
<iframe id="sketch" src="marvinjs/editor.html" style="width: 600px; height: 450px"></iframe>

The iframe keeps its id, size and styles; the script points it at the Athanor editor. The page's own code does not change:

MarvinJSUtil.getEditor('#sketch').then(function (sketcher) {
  sketcher.importStructure('mol', molfile);
  sketcher.on('molchange', function () {
    sketcher.exportStructure('mrv').then(save);
  });
});

If the page already has a real Marvin JS on it, MarvinJSUtil is left alone and the shim is reachable as AthanorMarvin.getEditor.

What maps

cxsmiles is written as plain SMILES, which is valid CXSMILES; the extension block is not.

Ketcher pages

A Ketcher page reaches iframe.contentWindow.ketcher, which no browser allows across origins. Ask the shim instead:

AthanorKetcher.get('#ketcher').then(function (ketcher) {
  ketcher.setMolecule('CCO');
  ketcher.getSmiles().then(console.log);
  ketcher.getMolfile('v3000').then(save);
  ketcher.editor.subscribe('change', onChange);
});

getSmiles, getMolfile('v2000' | 'v3000'), getCml, getInchi, getInChIKey, getSdf, getCDXml, setMolecule, generateImage (a Blob) and editor.subscribe('change') work. getRxn, getKet and addFragment are refused with a sentence saying what to use instead.

Every call is a message of the embed protocol: the shim never reaches into the editor's page, and the editor answers the embedding page's origin only.