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Ring Plate Visualisation

One diagram I've often wanted to make was filled-in rings in molecules :
Mainly for the purposes of highlighting rings without highlighting the atoms involved. This image was made using the CDK renderbasic module, and a small toy AWTRenderingVisitor that fills in paths. I'm not sure if the current one does this...

The gist for the main drawing method is here but is really just stuff seen before. The custom generator for rings is probably more interesting - if very simple - and is here. Note that it doesn't look too nice with inner-ring double bonds:

and would look nicer if the double bonds were symmetric.

EDIT : Coloring by ring equivalence classes didn't do what I expected...


Shouldn't all the outer rings be in the same class? Steran is how I expect, though:

Comments

Nice!

It makes me think, despite that Margin bug, maybe there is enough new stuff here to write up that paper... what do you think?
Rich Apodaca said…
Interesting idea - what would be some applications?
gilleain said…
Egon: Margin bug? This:

http://sourceforge.net/tracker/index.php?func=detail&aid=3062137&group_id=20024&atid=120024

or? If so, this is the two-pass system, which is more than just a bug :)

If we can find a way of unit-testing graphics, then that could definitely be publishable, as I think that a tested chemical graphics library would be of interest.
gilleain said…
Rich : Well, for any ring-finding algorithm, I suppose. I don't know what it would look like if you filled in a large ring that had smaller ones inside it.

A simple extension of the code I posted might color different ring equivalence classes (the SSSRFinder calculates these).

In general, you can highlight a set of atoms in a ring without confusion. Something like coronene could have all the outer rings highlighted, without the inner one.
gilleain said…
See this gist : https://gist.github.com/1023824 for the ring equivalence class code...

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