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This year, I've decided it's time to make more use of those other processors that my PC has. At some point, it gets embarrassing to see my single CPU job trundling along at its max speed, while 80 or 90% of the processing power is just sitting idle.My typical...
Let's suppose you need to iterate over the neighbours of an atom, and you want to know both the corresponding bond order and the atomic number of the neighbour. Given that toolkits typically provide iterators over the attached bonds or the attached atoms, but...
One of the consequences of last year's overhaul of handling of kekulization, aromaticity and implicit hydrogens is the ability to easily calculate structure hashes such as Roger Sayle's tautomer hash, which I wrote up on the NextMove blog a while ago.I routinely...

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In an earlier post, I showed the accesses in the first month for the Blue Obelisk and Open Babel papers from late last year. I should have stopped there. Instead I decided to see how the recent Avogadro paper compared (Update 15/09/12: thanks to Geoff for filling...
I've already mentioned using Open Babel for depicting with SVG. That's a handy way to view a large set of molecules; you can zoom in and out and so forth. Let's look at some more of the features, as I've just been adding them to PNG depiction from SVG. Let's...
The Blue Obelisk group was established at the Spring ACS Meeting in 2005. Following on from the presentation/poster I gave at PMR's Symposium in January, I put together an overview of the activities of the group over the past 5 years with help from Rajarshi...

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In January of last year I was invited to attend the Semantic Physical Science Workshop in Cambridge, England. That was a great meeting where I met like-minded scientists and developers working on adding semantic structure to data in the physical sciences. Peter...
I’ve been doing a little work to update iBabel, I’ve updated all the tools developed by Silicos-it to use the new names and options.The SVG support in Openbabel has undergone significant improvements due to the brilliant efforts of Noel O’Boyle...
I guess reader of my blog already heard about it via other channels (e.g. via Noel's blog post), but our second Blue Obelisk paper is out. In the past five-ish years since Peter instantiated this initiative, it has created a solid set of shoulder on which to...