My favourite chemistry things

Yeah, it’s my turn. Standing on the shoulders of ChemJobber, Azmanam, and ScienceBase, here’s list of things I like about chemistry. To put things into perspective first, a bit, I note that ChemJobber and Azmanam focused on wet-lab chemistry, and David on fancy molecules. Now, I am a theoretical chemist, and was thinking on what to orient the things I like, and on how general to make them. This meme is not easy, you now. But here goes:

4 minute read

How to use GitHub for [CDK|Bioclipse] code review

Triggered by posts in the past three days, I though about writing up a short tutorial on how to perform code review for existing code on GitHub. Therefore, this applied to CDK and Bioclipse source code, many but will work for any project hosted in GitHub. Even if it is not, you could consider putting up a copy there yourself. This example will demonstrate the procedure on CDK functionality in Bioclipse in the bioclipse.cheminformatics repository.

2 minute read

GitHub simplifies code review and leaving comments

The workflow here is that the proposed patch gets uploaded to a GitHub branch or fork; the code reviewer is made aware of the patch, and goes to the commit page on GitHub, and hovers over the line numbers and clicks the ‘Add comment’ button and leaves a comment; the reviewer informs the author, and the author updates his patch.

less than 1 minute read

Web 2.0 technologies in Student Assessment

Below should show up the wave (that is, if you have a Google Wave account), about a piece I am writing for a course on PhD Supervision I am following. The aim is to dig up old standards and how they apply to Web 2.0 technologies, including wikis, waves, blogs, source code repositories etc.

less than 1 minute read

CIP rules #2: parsing @ and @@ from SMILES

I recently wrote about a project for a (partial) CIP implementation. This implementation is in place, and we are working towards setting up an extensive test suite. The data set we had in mind was available as SMILES and as MDL molfile. Now, the latter does not really specify the stereochemistry of the tetrahedral centers, and relies on wedge bonding. Actually, a few years ago Jonathan Brecher wrote up the IUPAC recommendation for the use of the wedge bond for chirality specification (doi:10.1351/pac200678101897), with 74 pages of rules and examples, like the following (copyright by authors or journal; I’m claiming fair use):

less than 1 minute read

Wondering who will be the 100th Blue Obelisk eXchange user...

 

less than 1 minute read

Chem4Word goes Apache 2.0

Early March I reported about Konstantin’s JChemPaint-based chemistry plugin for OpenOffice, but there is (friendly) competition: Chem4Word. Being for Microsoft Word, the plugin only works on top of proprietary software, unfortunately; therefore, I cannot tell you if Chem4Word release is any good, but what Jim has showed me about a year ago, it is pretty cool. Another big difference is that Microsoft gave the Chem4Word a big grant, and Konstantin does not have such funding, AFAIK, and relies on community support.

1 minute read