[ghemical-devel] about gnome2, and moving to a single "project" class.

[Geoff Hutchison]

> So, when planning this, it soon became evident to me that the best way of
> implementing the mixed models would be to combine all our current 3
> "projects" to a single "project". This single project would be like our
> current molecular mechanics project (containing atom and bond objects).

Actually, Adam Tenderholt, an undergrad here at Northwestern has been
hired to do this very thing. He has some code for a "UniModel" that's
already assembled, based on a "Monomer" as an intermediate structure
between the molecule and the atoms. So a collection of atoms (e.g. an
amino acid) could be a "monomer" and treated together.


> actually compiles and starts.  :)  It basically just compiles and starts
> really, so for example you can't compute anything with it yet.

Adam has many things working now--the open/save works through Open Babel
and you can draw atoms and bonds directly.

> So, what would be the future of these modifications? As I decribed above,
> it seems to me that this approach might lead into simpler user interface
> and code in the future, but it will also take some time for me to clean

Yes, we definitely agree, but hopefully with multiple people working on
the same direction, it might go faster. I thought that Adam had contacted
you about his work in this direction, but I guess not. Hopefully you two
can pick up and collaborate some?

-Geoff