Just a heads up that I made some progress on the selection tool for
Avogadro this weekend, I have basic toggling working, and some OK
rendering (just turns selected atoms blue at this stage, but adding
transparency etc should be easy enough in the future).

I have been working on adding an array to the molecule class to
support this, adding some simple rendering code to ball and stick, and
developing it in a tool plugin. I think integrating with the molecule
is much nicer than how we did it before, and it seems like it would be
simple to add to CJSON.

I was going to look at adding a selection box next, and deletion of
selected atoms. I also need to add undo/redo support, if anyone is
interested in the half-working version I can share it on my fork of
avogadrolibs, otherwise I will see what I can do to get it closer to
being merge ready. I will try and get some time into updating issues.

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