Change Template>Ligands to Fragments and Build>Insert>Fragment to Molecule

[matterhorn103]

Fragment to me implies part of a molecule, rather than a full self-contained one. Adding these to an extant molecule is what the Template tool does via Ligands.

Since the fragments from Ligands can be added to any molecule, not just metals, it is useful for adding e.g. acetyl groups to sugars, and calling it ligands hides this fact.

The source for the contents of that tab is also the OpenChemistry/fragments repository.

Meanwhile Build|Insert|Fragment... allows the insertion of full molecules, not attachment to current ones. It is sourced from OpenChemistry/molecules.

For consistency I suggest calling the Ligands tab of the Template panel Fragments, and the menu option Build|Insert|Molecule...

If this is agreed on then I'll look at changing it myself.

[ghutchis]

Seems like something to post on the forum https://discuss.avogadro.cc/

Build -> Insert -> Molecule is fine with me.

Not quite as sure about "Fragment" vs. "Ligand" in the template tool... ligand seems somewhat better to me, in part because many of the categories are ligands.

Maybe the solution for discovery is to have 3 tabs: "Centers", "Ligands" and "Fragments" or "Functional Groups"

[matterhorn103]

Sorry, I am often unsure when a forum post is better to promote discussion and when it is better to just open an issue to save you a job.

Maybe the solution for discovery is to have 3 tabs: "Centers", "Ligands" and "Fragments" or "Functional Groups"

That would also be a sensible way to do it.

[ghutchis]

No worries. I've been trying to keep "things that need discussion from many people" on the discussion forum and "tickets for accountability" here on issues.

I've noticed that more casual users don't follow GitHub.

[ghutchis]

Let me know if that PR does what you suggested...

[ghutchis]

Oh, you wanted the molecules piece too..

Do you think I should move Build => Insert => Molecule to File => Import to match the Crystals dialog?

[github-actions]

Here are the build results
Avogadro2.AppImage
macOS.dmg
Win64.exe
Artifacts will only be retained for 90 days.

[github-actions]

Here are the build results
Avogadro2.AppImage
macOS.dmg
Win64.exe
Artifacts will only be retained for 90 days.

[matterhorn103]

Let me know if that PR does what you suggested...

This looks perfect this way I think, yeah. :)

I wonder if maybe under Templates > Centers > Coordination: the "1: Linear" option should be called "1: Terminal" to avoid having both it and "2: Linear" described as being linear, which leads to slight confusion.

On a more philosophical level, can an atom with a single bond even be considered a linear geometry?