Re: [Avogadro-Discuss] SUBSTITUTE atom by fragment

[Geoffrey H. <ge...@ge...>]

> We are currently developing the Wiimote extension (Michael Gadroy has been working on that for 8 months in our lab., and most of the manipulation, rotation, selection, construction, measure tools

Cool! I'm glad to know that code is being updated. It seemed like a great idea, so I'm looking forward to seeing the possibility.

> 2) select a "SUBSTITUTE atom by fragment" menu
>   (as for INSERT using the "Building" menu)

This part is tricky. At the moment, there is no signal that the user selected anything. So right now, we can't change the menu item.

> 3) choose a fragment in the library 
> 4) the selected atom will be substituted by this fragment 

I've been imagining an interface with a tool -- the user clicks on an atom, which is immediately replaced by the fragment. For the tool, the user could also select a particular atom in the fragment for bonding (e.g., axial vs. equatorial positions in a cyclohexane). GaussView and Spartan function along these lines.

But I did take some time today and code an improvement to the insert fragment and SMILES commands which functions the way you describe. It's not as flexible, since it automatically picks the first atom in the fragment for bonding. But it works and will serve as the start of the tool.

If you use a Mac, it will become part of the nightly unstable builds. Otherwise it will probably take a few days before it becomes part of the "master" development code.

> In my opinion, the "fragment" word (french version of Avogadro) 
> is not exactly appropriate

I haven't looked at the French translation. In English, we're trying to use the sense of "a small piece" for fragment (i.e., it may be an isolated molecule, but it's intended to become a small piece of the whole).

Certainly we're open to patches, either to the insert commands or to the translations!

> Once more, thanks for developping Avogadro which
> is a very helpful tools both in research and education !

Our pleasure!

Best regards,
-Geoff