Getting Avo2 to release

I’ve been trying to sift through Avogadro v2 and trying to determine what needs polish and what are missing features needed for a release.

I’d like to outline things that I think are critical versus “nice to have, but could wait for 2.1”

Thoughts? Concerns? Something I’ve missed?

-Geoff

Critical:

  • Selection Tool / Extension
    … requires a concept of a selection (e.g., in the widget)

  • Properties
    … atom, bond, angle, torsion
    … including editing properties (and saving to text files)

  • insert fragments
    … molecules, DNA, peptide
    … integration with MongoChem for molecules & crystals?

  • Rendering features
    … labels, hydrogen bond, forces, dipole, stick, etc.

  • Constraints / AutoOptimize
    … there are ways to handle the optimization, but freezing / constraints are needed
    … could include symmetry constraints (e.g., libmsym)

Nice to Have:

  • Visual Cues / Eyecandy

  • Fragments / residue support
    … rendering cartoons, ribbons, etc.

  • Spectra / Orbital panels

  • Nanotube builder

  • Nanoparticle builder

  • Centroids (center of atoms, center of mass)

  • Zero order bonds

Thoughts? Concerns? Something I’ve missed?

Oh, I forgot color schemes and custom colors. My feeling is that can fall to “nice to have for v2.1”?

-Geoff

On Wed, May 27, 2015 at 3:55 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

Thoughts? Concerns? Something I’ve missed?

Oh, I forgot color schemes and custom colors. My feeling is that can fall to “nice to have for v2.1”?

I have some time this next couple of weeks to take a stab at some
pieces. I think the critical and nice to have may vary a little
depending on person. I will make a new release soon (0.8) as I would
like to get more people testing stuff. Selection and residues, along
with some rendering features seem most critical to me (we have stick
but it has a rendering bug I need to dig into). I would like to expose
the transfer function editor from VTK, and finish off the volume
rendering piece but would put that firmly in nice to have.

This has languished more than I would like, so apologies from me for
not having as much time as I had hoped. There are some great features
in there, but UI polish is needed to make it more accessible. It is
orders of magnitude faster loading initial data, and rendering it, for
large systems, but the interface is missing some key pieces (some
already fixed) which led to me delaying 0.8.

I think your list is a good yard stick, and just like with 1.0 we will
possibly wait too long, but know it when we see it. I had hoped to
have it a year ago, and am determined to make it happen. I think a
test run on Qt 5 deployment will be valuable (it was working for me on
Mac and Windows when I tried it last time.

I am blown away by over 600,000 downloads since our first release of
Avogadro, and over 400 citations of our paper. I want to get some
momentum going again, and hope we have even more ideas to put into a
Google Summer of Code proposal next year.

Best,

Marcus

Selection and residues, along with some rendering features seem most critical to me (we have stick but it has a rendering bug I need to dig into).

I’d put selection slightly above residues because I think it’s critical for copy/paste/clear and moving fragments. (Which I guess also means that inserting fragments is a needed piece.) Indeed, I think selection affects a lot of tools and extensions, so that’s my preference.

I would like to expose the transfer function editor from VTK, and finish off the volume rendering piece but would put that firmly in nice to have.

Oh, I think I’d call the “transfer function” the color gradient (e.g., blue = positive, red = negative, white or green is 0, etc.) Yes, I think that would be very nice to have, but it wasn’t in 1.x, so I’d hardly consider that a showstopper.

Volume rendering… well, you know that I’m a big proponent and I’d love to see that happen soon. Realistically, I don’t think it’s critical either.

I’ll put the list up online somewhere tonight…

-Geoff

On Thu, Jun 4, 2015 at 4:07 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

Selection and residues, along with some rendering features seem most critical to me (we have stick but it has a rendering bug I need to dig into).

I’d put selection slightly above residues because I think it’s critical for copy/paste/clear and moving fragments. (Which I guess also means that inserting fragments is a needed piece.) Indeed, I think selection affects a lot of tools and extensions, so that’s my preference.

Agreed - wasn’t really ranking, but selection is certainly more
critical than residues. I really don’t think we are that far apart,
and value the input on priorities. If others have feelings it would be
great to have them.

I will do selection first, but would like to follow that quite quickly
with fragments, residues, monomers, etc.

Marcus