Marcus D. Hanwell's Blog

I am very pleased to announce that Avogadro has been nominated as a finalist in the SourceForge community choice awards this year. We are in the "Best Project for Academia" category, and I would like to encourage you to vote for Avogadro.

This is a real honour for all of us, and I appreciate all of you who nominated Avogadro. We are all pushing very hard on polishing Avogadro, getting ready for our 1.0 release. It would be absolutely amazing to see Avogadro win this award, so please vote for us.

There are also some other really nice projects in there too, such as Lancelot, ClamAV, phpMyAdmin and RepRap. So please take a few moments to place your vote, and tell your friends!

Update: You can vote even without a SourceForge account - just enter your email address and verify your vote.

Exactly two weeks ago today my son was born, weighing in at 8 lbs 13 oz and measuring 21 inches long. Louise and I have named him William Aaron Alexander Hanwell, our new addition has been thriving after a bumpy start. I would like to claim first foetal attendee of a KDE conference, getting him off to a brilliant start listening to some great technical talks in Jamaica. I know most people play classical music to their unborn children, but we like to be different I need to find him a KDE baby grow!

You can see him in the above photos just minutes after his birth, and a little more relaxed the next day in his hospital crib. Not wanting to be too run of the mill he was consistently breach, delivered by C-section and had his cord wrapped around his neck 2.5 times. Not a problem for that kind of delivery, but it would have been had we had the natural birth we were hoping for. As he was born in the US he also manages to get dual nationality (US by birth, UK from us), whilst his poor old Dad is still waiting to hear back about his H-1B visa...

I think three days prior Carsten's wife gave birth too, and I believe Mauricio will also be growing his family later this year. So the KDE Edu developers all seem to be expanding their families this year, I guess the greater question is whether this was a coordinated effort As with all true geek babies I will be setting him up with his own blog and online photo album, mainly so that our family and friends back home will be able to keep up with him as he grows.

So far I am really enjoying being a new father, although aware that this isn't the only big change over the summer!

Over the last few days we have been working on improving the look and feel of the Avogadro user interface. We owe both Qt Software and the Oxygen icon team a lot for making this process a lot easier. Avogadro uses quite a few Oxygen icons that we have taken and in some cases adapted slightly.

The sliver of screen shot above shows our tools tool bar, along with the tool and display settings buttons. We are pretty happy with the majority of the icons, which are (from left to right) draw, navigate, bond-centric manipulation, atom centric manipulation, selection, auto rotation (animated rotation about axes), auto optimise (continuous optimisation of the molecule geometry), z-matrix, measure and align tools.

I would really welcome any suggestions and/or icon submissions for the auto rotate (the spinny thing near the centre), and the auto optimise (the wand with the circle) tools. I think auto rotate is OK, but it would be better if it conveyed more of a three dimensional rotation. The auto optimise wand is perhaps the worst as it does not suggest optimisation of the geometry, but I am not sure what would. Do any of you more creative types have any suggestions?

I also wonder if there are nice icons we could use for tool and display settings, or a way to make those buttons smaller without losing discoverability. I look forward to hearing people's thoughts. As this is what people see when they first open Avogadro we would like to make the interface as inviting and intuitive as possible.

Yesterday I tagged the Avogadro 0.9.5 release, you can grab the latest downloads from here. Life has been hectic this last couple of months, and to be honest I have not gotten as much done as I would have liked. Still there are some great additions such as the experimental cartoon ribbon display ported by Tim from the Zodiac Zeden project.

Geoff also worked on getting more screen real estate for the actual display, after we bounced some ideas around over the last few months. I think that looks great, and have always tried to ensure the maximum amount of screen space was devoted to displaying the molecule. I still have a few more ideas, but fear I do not have the time to implement them. Geoff also added a new peptide builder and David has been working tirelessly on plotting spectra.

I have been working on decidedly less glamorous and less visual aspects of Avogadro. This includes improvements to our build system, I added the infrastructure required to find and build plugins/applications against the system installed Avogadro library. I also uploaded a few examples to GitHub, and David is actively working on an external plugin for a summer project.

I worked on getting a CMake project that included and compiled both Avogadro and OpenBabel. I then turned my attention to making a relocatable, self-contained app bundle for the Mac. This is working quite well, although there are a few parts of the build system I would like to clean up. It does mean we have relocatable applications that can run from a USB stick on both Windows and Apple systems now.

I crushed quite a few bugs too, worked on API improvements and fixed Noel's long standing feature request - to disable the visual cues when navigating around a molecule. The original Windows installer shipped with a data loss bug, when saving a molecule the original could be erased and you would be left with a zero length file. This was a Windows specific bug that slipped through, I spent half of today tracking this issue with a few other Windows bugs and updated installers have been uploaded (Tim made the Python enabled installer). Please ensure you update to Avogadro-0.9.5-win32a.exe or Avogadro-0.9.5-python-win32.exe. Hacking on Windows has to be one of my least favourite activities, and I need a couple of days away from that whole platform before I can go back and finish some of the work I have been doing...

We are pushing to a 1.0.0 release, targeted for July. We would appreciate feedback on the interface, bugs encountered, the public API that is installed along with any other suggestions or offers of help. Our translations are now doing very well too, and any help improving them further would be appreciated.

Enjoy the new release, another is likely only a week or two away as we crush the remaining bugs. I am also fighting to find time to implement a few more features I would really like to see in Avogadro 1.0.0.