Thursday 24 March 2011

Announcing 2nd Open Babble - Pre-registration now open

Pre-registration is now open for the 2nd Open Babble, a hands-on Open Babel workshop presented by Open Babel developers. This will take place on July 5-6 2011 at the Unilever Centre in the Dept of Chemistry, University of Cambridge, UK.

The workshop will start on the afternoon of the 5th July, and finish on the evening of the 6th. The precise topics to be covered will depend on the attendees’ interests but we anticipate covering topics such as how to get the most from the Open Babel command line applications and the GUI, to writing Python scripts and developing software based on the Open Babel library.

Since only 20 places are available, we are running a pre-registration process to select a diverse range of attendees, from novices to expert users, and from both academia and industry. The registration fee will be €70 for academics, and €220 for industry attendees. This includes one lunch and dinner, but does not include accommodation.

We also note that sponsorship opportunities are available.

To register your interest in attending, please email before April 22nd with the following information:

Name: _______________
Position: ______________ (e.g. PhD student)
Address: ___________________
Email: _________________
Registration fee: €70/€220
Reason that you should be selected to attend (max three sentences):
Topics you would like covered: ____________________________________________

Noel O'Boyle
(On behalf of the Open Babble organisers)

Monday 21 March 2011

Confab, a systematic conformation generator, published in J Cheminf

My paper on Confab has just been published by the Journal of Cheminformatics. Confab is a systematic (and exhaustive) conformation generator that uses a torsion-driving approach to generate all diverse (by RMSD) low-energy conformers.

Confab - Systematic generation of diverse low-energy conformers NM O'Boyle, T Vandermeersch, CJ Flynn, AR Maguire, GR Hutchison. Journal of Cheminformatics 2011, 3:8.

The software itself is available from

Here's the abstract of the paper:
Many computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-energy conformers according to a diversity criterion.

Confab generates conformations using the 'torsion driving approach' which involves iterating systematically through a set of allowed torsion angles for each rotatable bond. Energy is assessed using the MMFF94 forcefield. Diversity is measured using the heavy-atom root-mean-square deviation (RMSD) relative to conformers already stored. We investigated the recovery of crystal structures for a dataset of 1000 ligands from the Protein Data Bank with fewer than 1 million conformations. Confab can recover 97% of the molecules to within 1.5 A at a diversity level of 1.5 A and an energy cutoff of 50 kcal/mol.

Confab is available from

Monday 14 March 2011

Can we use game consoles for chemistry? Yes WiiChem

I've written about using the Kinect to control Jmol, but there's another game console gadget that's been around for some time that offers similar possibilites - the Wii Remote or more simply, the "Wiimote".

A few days ago, Eric Henon and Mickaƫl Gadroy of the University of Reims announced the WiiChem project on the avogadro-discuss mailing list:
We are pleased to announce that it is now possible to carry out the Wiimote possibilities into Avogadro.

The Wiimote gives the opportunity to use a cheap, easy and flexible device for educational purposes for example. By pointing a Wiimote at a screen you can create, rotate, substitute atom by fragment, ... molecules. Also, you can use it with projector.

Anaglyph (Red-Cyan)/3D possibilities have been implemented.

The feeback (rumble functionality) can be used to check « on the fly » proximities between the molecular system and the manipulated atom.

This is still a Beta version. The src plugin as well as all instructions to compile it are available at :
It would be nice to finally see one of the open source 3D viewers come with this functionality out of the box, so this is a very exciting development.

For more information or if you want to get involved, see the Avogadro mailing list, the github repo, or the website for the project (English/French).

Image credit: maury.mccown

Friday 11 March 2011

Open Babel book now available

The image above says it all. We've packaged up the Open Babel user documentation as a 160-page book and it's now available for purchase from Lulu at the cost price of €7.48 (since the postage may cost almost as much, you may want to consider buying Egon's and Angel's books at the same time).
Support independent publishing: Buy this book on Lulu.
This is the same documentation available from, but we've made it into a quarto-sized book (roughly the same aspect ratio as Letter, but somewhat smaller) with a glossy paperback cover. I'm very happy with how it's come out (apart from some minor things) - thanks to LaTeX it looks pretty professional.

It'll be interesting to see how many copies of this are sold, seeing as we are giving the content away for free electronically. Personally I find it much more convenient to have a book than to print out a PDF. And I should point out that we welcome further contributions to the documentation, so if you want to see your name up there in lights...I mean...on the front of a book, start sending in your chapters now!

Technical notes: The LaTeX for the PDF was generated from reStructuredText using a development version of Sphinx 1.1 so that URLs would be included as footnotes. The source is stored in a Mercurial repository at BitBucket. Feel free to fork to fix typos!

Image credit: Tim O'Sullivan

Friday 4 March 2011

Open Babel summer of code - Undergraduate project available on parallelisation of forcefields

The Irish Centre for High End Computing (ICHEC) has funding for a 10-week summer project for a senior undergraduate student in Open Babel development:
OpenBabel: optimisation of the MMFF94 routines using OpenMP and OpenCL

At the heart of many computational chemistry modeling suites are the forcefields and their associated energy and gradient functions. One such forcefield, MMFF94 (Merck Molecular Force Field 94), was developed by Thomas A. Halgren at Merck and has become one of the most widely used in the drug design domain.

OpenBabel is an open source cheminformatics project and MMFF94 is one of many forcefields it provides. OpenBabel has been downloaded over 164,000 times and is used by over 40 related projects.

This project will involve the optimisation and parallelisation of the MMFF94 functions within OpenBabel and will be conducted in collaboration with Dr. Noel O'Boyle at University College Cork.

The project involves parallelisation of the forcefield code, and potentially porting it to the GPU using OpenCL. There is a lot of expertise at ICHEC in these areas.

If you know someone in chemistry, physics, or computer science (from any country) who might be interested, I'd appreciate if you could point them to this blog post or the ICHEC website. The closing date for application is 13th March.

Thursday 3 March 2011

Using Kinect to control Jmol - Part III

Part I, II.

The final step is to get hacking on Jmol itself. We need to add support for reading hand locations from the OSC port, and then to spin or rotate the molecule based on the x, y, z coordinates of the hands.

(1) Follow the instructions on the Jmol wiki to install Eclipse, checkout the Jmol code from subversion, and compile it.

(2) Deep down in Jmol/src/org/openscience/jmol/app, you will find Replace this with one of the versions I've placed in a github repository. The master branch is simply the original; the other branches are different interfaces. (This code is based on work by some combination of Dan Hagon, Sam Adams and Bob Hanson.)

(3) These files have an additional dependency on JavaOSC. You can find the jar in the lib directory of the available here. To add the jar file to your CLASSPATH in eclipse, right-click on Jmol, Properties, Run/Debug Settings, Jmol, Edit, Classpath, Jmol, Add External JARS, and navigate to the Jar file (oh Eclipse, how we love you).

(4) Run Jmol from inside Eclipse, max out the screen, and wave your arms around.

And so there you go...hopefully this will get other people interested in hacking some Kinect into chemistry software. Only this last post was Jmol-specific; the general idea could be used to control any software.