Embedding Molvwr into your site is totally free and very easy. The most simple way is to add the script "molvwr-bundle.js" to your page, just like this:
<script src="lib/molvwr-bundle.js"></script>
This script contains a bundle of
Molvwr,
Babylon.js (a WebGL 3D Engine) and hand.js (a polyfill for pointer events that enables touch interaction).
You could also add the different files separately if you would like to use Babylon somewhere else in your site.
When your script is ready, add a bloc in your page with a "data-molvwr" attribute containing the path of your molecule file :
<div class="mol mol-left" data-molvwr="mol.sdf"></div>
Now you just need to call "Molvwr.process()" to have your bloc turning into a 3D molecule
<script type="text/javascript">
document.addEventListener("DOMContentLoaded", function() {
Molvwr.process();
});
</script>
The "process" function can be called without parameters, or you could explicitely provide an HTML element (or an array of elements).