Sets of plugins for Avogadro

Development
1

Avogadro is great software, covering many fields of chemistry. Almost every release adds new extensions and/or display types.

With every new plugin its GUI becomes larger and more complicated for users, application eats more and more memory and startup time increases, list of display types has scrolling bar, etc

Of course, advanced user knows, that it’s easy to remove unnecessary plugins. But newbie will be afraid of hundreds of menu items :slight_smile:

I propose to create standard sets of plugins, making Avogadro usable for distinct fields of chemistry. User will choose one of them, e.g., in tab General of Avogadro Settings or in First Startup dialog (needs to be created)

Examples of plugins’ sets:

Small Molecule Crystallography

Display Types:
axes
dipole
hydrogen bond
label
polygon
wireframe
VdW spheres
stick
surfaces

Tools:
Align,
AutoRotate,
Measure,
Navigate,
Selection

Extensions:
animation
Hydrogens,
mol. properties,
network fetch,
pov-ray
properties,
selections,
super cell,
unit cell,
surfaces

Large molecule Crystallography & Biochemistry

Display Types:
axes
cartoon
dipole(?)
hydrogen bond
label
polygon
ribbon
ring
wireframe
VdW spheres
stick
surfaces

Tools:
Align,
AutoRotate,
Measure,
Navigate,
Selection

Extensions:
animation
mol. properties,
insert peptide
network fetch,
pov-ray
properties,
selections,
unit cell,
surfaces

Quantum Chemistry

Display Types:
axes
dipole
force
hydrogen bond
label
overlay
VdW sphere
stick
surfaces
wireframe

Tools:
all

Extensions:
all with exception of:
-insert peptide
-network fetch
-super cells
-unit cells

School Chemistry

(on your choice)

All plugins

(no comments)

Custom

(on choice of user)

Explanation for drawing: crystallographers don’t need to change molecules with Draw, but Adding/Removing Hydrogens can be useful

Also I propose to split filter Common molecule formats into field-dependent file type filters as
Common QC formatc (*.inp, *.in, *.log, .out, …)
Common crystallography formats (.cif, *.res, *.pdb, …)
Common 2D molecule formats
…

–
Regards,
Konstantin

2

Konstantin Tokarev wrote:

Avogadro is great software, covering many fields of chemistry. Almost every release adds new extensions and/or display types.

With every new plugin its GUI becomes larger and more complicated for users, application eats more and more memory and startup time increases, list of display types has scrolling bar, etc

Of course, advanced user knows, that it’s easy to remove unnecessary plugins. But newbie will be afraid of hundreds of menu items :slight_smile:

This is something that we have discussed several times before. I think
it should be a new feature for Avogadro 1.2. When I first started
working on Avogadro this was not an issue, and in many ways it is great
to have this problem.

I have made master version 1.1 now (unstable - open for new features).
So this feature could be worked on in there. We can make some 1.1
releases once there are new features that require further testing. For
now I think this could be achieved using an external plugin possibly too.

We need to be careful here not to offer so many options in
configurations so as to cause confusion too. We had always envisioned
even individual universities distributing custom versions of Avogadro
which were tailored to their courses.

Marcus

3

I propose to create standard sets of plugins, making Avogadro usable
for distinct fields of chemistry. User will choose one of them,
e.g., in tab General of Avogadro Settings or in First Startup dialog
(needs to be created)

I think we may want this to be a separate tab in the Settings window.
See, the underlying code is based on the QSettings for Avogadro. So
your idea can implement a few related features too:

  • reset settings to default
  • import/export all settings (e.g., for setting up a lab of computers
    with the same loaded plugins, etc.) to a file.
  • load sets of plugins for “modes”

Also, Marcus and I started on some code which would read/write
settings (e.g., rendering colors, etc.) from a CML file.

So if this is something which interests you, I can certainly help
point you in the right directions. It’s doable, but will require some
work.

Common QC formatc (*.inp, *.in, *.log, .out, …)
Common crystallography formats (.cif, *.res, *.pdb, …)
Common 2D molecule formats

This is a good idea, and something we can do for 1.0.1 – separate
from the plugin/settings idea. I do think we should keep a “very
common” general list, e.g., .pdb, .sdf, .mol, .xyz, and of course .cml
for us.

If you make an initial patch for this with your suggestions, I’ll help
you refine it.

Cheers,
-Geoff