Re: What should a Nature Chemistry paper look like?

Neil wondered “what a Nature Chemistry paper should look like”, and asked the following questions. Below are my answers.

3 minute read

Wicked chemistry and unit testing

After a discussion on starting development releases for CDK on cdk-devel, the discussion continued on the state of the CDK atom typer. Dan and Rajarshi have done tests in the past against PubChem and its DTP/NCI subset. Rajarshi made his analysis part of CDK Nightly, and provides but a summary (which seems broken: zero fails) and a detailed list.

3 minute read

Comparing JUnit test results between CDK trunk/ and a branch #2

I reported earlier on how to compare unit test results between CDK trunk and a branch. Later, I noted that the diff typically overestimates the fail count, when unit tests had been moved to a different module. Therefore, a sort has to be added. The code is also updated for the SVN directory restructuring:

1 minute read

JChemPaint for Bioclipse2

Today Ola, Jonathan and I have a mini-hack session on getting JChemPaint support ported from Bioclipse1 to Bioclipse2. And, we made some progress:

less than 1 minute read

Blog Comments? No, Peer Reviews!

Via Carbon-Based Curiosities’s blogroll I found a number of new blogs (on top of the list I posted yesterday), and just added them to Chemical blogspace. This is something I found in Infiniflux!:

less than 1 minute read

Comments on 'Rethinking software access'

bbgm was rethinking software access. The blog observes:

3 minute read

More CDK-Ruby users...

Via Rich’ blog, I was informed about the work by goesLightly on CampDepict, a Ruby-based application which uses the CDK for SMILES parsing and 2D diagram generation. With cdk-20060714.jar it’s using pretty ancient code, and I have not seen a screenshot.

less than 1 minute read