Hi Marcus,

As I've mentioned before, I'm working with Paul Boone here at Pitt on a new 
script interface in Avogadro 2. Scripts (not just Python) will have a similar 
API to the input generators, but will hand back a modified molecule to 
Avogadro. Eventually, we'll implement a download-from-GitHub feature.

I'm trying to do the least amount of refactoring:
- Right now it seems like "Paste" doesn't actually modify the molecule - 
instead, a new one is created. I'd like to adapt the paste command to work like 
Avogadro v1 -- add more atoms and bonds to the current molecule

- I still have no idea how the UI for the molecule list is supposed to work. I 
realize this is a Mac bug, but it seems like there should be a way to "merge" 
or "split" those entries. However, since the undo stack is maintained by the 
RWMolecule, I'm unclear on how you would implement undo/redo for those concepts.

- I'm going to add selection to the RWMolecule and CJSON (i.e., which atoms are 
currently selected). This will enable "regular paste" by including an append() 
method with undo/redo support. Selections will also have undo/redo support 
(i.e., the before and after bit vectors of selected atoms).

- I'm going to take the InputGeneratorWidget out of avogadrolibs / molequeue 
and put it into qtgui/ as InterfaceWidget. It will handle both input generators 
and the new action scripts (i.e., parsing the JSON from the scripts) - I will 
probably add small subclasses to handle the two different types, e.g., the 
preview text in the input generators, etc.

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