Yes, many Javascript libraries involvedin Ketcher -- things may get 
complicated.

@Philip:

The design of Ketcher interface is not very flexible -- I don't like 
much these systems whose functionality relies on "modern html" 
(javascript, html5 canvas, SVG) and yet rely on a fixed-size 
interface based on tables --which are systematically despised by the 
html5 gurus.
It would be much nicer to have an interface whose elements may be 
programmatically included or excluded and whose design, size etc. may 
be changed e.g. by CSS.
Some time ago I managed to trick Ketcher into a reduced-size-icons 
version that seemed to retain all functionality:
http://biomodel.uah.es/en/DIY/Ketcher/

I think it was via CSS rules imposed over the default design, but 
don't remember now for sure.


@Javier:
The most chemically-savvy drawing system in webpages for me is 
JChemPaint, a Java applet. If that does not do what you want, I doubt 
there is another one that will. 
http://biomodel.uah.es/en/DIY/


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