The CDK data model #1

The Chemistry Development Kit has a rich set of data classes, each of which is defined by an interface. While the classes for atoms, bonds and a connectivity table are fairly straightforward, but beyond that it is sometimes not entirely clear. I will now discuss all interfaces in a series of blog items. I’ll start with the IChemFile. Christoph, please correct me if I move to far away from our Notre Dame board sketch.

2 minute read

The Open Science Notebook 10 years ago

So, with all these people blogging about the Open Science Notebook (yes, each word is one distinct blog) it is worth looking back in time. To make clear what I put under the OSN: a notebook in which experimental details and outcome are written down. So, what did the OSN look like almost ten years ago?

1 minute read

CDK Literature #2

Second in a series of articles summarizing articles that cite one of the main CDK articles for CDK News. The first CDK Literature was already half a year ago, so it was about time.

2 minute read

Inter- and Extrapolation: the NMR shift prediction debate

Chemical blogspace has seen a lengthy discussion on the quality of a few NMR shift prediction programs, and Ryan wanted to make a final statement. Down his blog item he had this quote from Jeff, discussing the use of the NMRShiftDB as external test set:

4 minute read

That big pile of paper...

Everyone of use knows that big pile of paper on your desk that contains the things we want to read, scan or just browse. I even have an electronic equivalent. Another pile contains leaflets and glossy folders from conferences, like the ACS meeting in Chicago. OK, going to get rid of those last ones, and will shortly put the links here.

1 minute read

Standing on the shoulders of ... the Blue Obelisk

The Seven stones wondered what to do with a petaflop in science, in response to Declan’s The petaflop challenge in Nature. Declan discusses in this commentary the increase in computing power and the necessity of parallel programming to make use of it. Now, I do have some ideas (e.g. enumerating metabolomic space, mining the RDF graph of our collective biological and chemical knowledge base for the one hundred most supported contradictions), but that is not what I want to talk about. It is this fragment from Declan’s piece:

2 minute read

Atom typing in the CDK

Atom typing is one of principal activities in chemoinformatics. Atom types provide additional information that cannot be derived from the connection table that is being used, or may define what force fields terms should be used. This makes perception of atom types very important.

2 minute read