On Dec 8, 2007, at 7:20 PM, Tim Vandermeersch wrote:
solvent all atoms residues named HOH. (or do we want code to find
these?)
This will need to be written as code. You personally may be working
with residues that have nicely named HOH bits. Others (e.g, Donald or
myself) are not so lucky. Solvent molecules do not come tagged. And
solvent may be more than just water. Someone might want to pick from a
set of solvent options.
So I think the best way to handle this is to have a popup menu of
solvent options and these get translated into SMARTS, plus some code
to make sure the SMARTS matches a solvent molecule, rather than
something inside a larger molecule.
possibility to hide items from the menu’s so you can only display the
items you use? (or planned)
One of my original ideas was that you’d have “selection plugins.”
Donald convinced me that you could do this inside the Extension
framework. But I suspect we’ll want to split out multiple extensions
and let people turn them on and off.
Yes, it all looks very nice. But are there any guidelines we should
follow, so everything has the same way of doing something. If it gets
out of hand, we could always assign a form designer
I don’t think we’ve gotten to the point of writing guidelines.
Sometimes it helps to work on enough functionality that you’ve tried a
few things that work and a few things that don’t work. We should write
up some guides pretty soon, though.
Cheers,
-Geoff