First off, apologies that your post got stuck in the spam queue for a few days. 
If you subscribe to the list, this won't happen.

>               I try to develop a plugin where the coordinates of atoms will 
> be frozen in the Z axis.

This feature already exists, although it may not be as easy-to-use or 
discoverable as one might like. The force field extension offers a constraints 
dialog. See Extensions -> Molecular Mechanics -> Constraints.

What might be nice is for this dialog to pick up on selections -- in other 
words, select some atoms, pick "freeze Z" and it freezes all the z-coordinates.

> I was wondering if there was a way to interact with tools to change their 
> behavior, or if I need to create a new tool from scratch to do that.

You can either add code to existing tools or implement a new tool. If this is 
the feature you want, I'd probably keep to the existing tools and modify the 
force field extension code.

> Also, is it possible to force glwidget to use only a specific tool (I think 
> of disconnect() )?... I am pretty new with Qt so it is not really a natural 
> way of thinking for me. Thanks for your help.

Do you mean you want GLWidget to change the current tool? Yes:
GLWidget::toolGroup()
http://avogadro.openmolecules.net/api/dev/classAvogadro_1_1GLWidget.html
// Change to the navigate tool if loaded
glwidget->toolGroup()->setActiveTool("navigate");

We'd be happy to help -- subscribe to the list and post whatever questions you 
have at getting started.

Hope that helps,
-Geoff
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