PMD code checking: checking for programming against CDK interfaces

I wrote recently about programming against interfaces, which led to some discussion. Rajarshi commented:

less than 1 minute read

Cleaner CDK Code #6: set the CDKException's cause Exception

For about two weeks now, I am working on fixing a bug in the nonotify module: the classes were still sending around change events. I decided to finally do it the proper way: sending around change events is extra functionality, so the data module should extend the nonotify module and not the other way around, as in CDK 1.2 and CDK 1.3 up to now. There was a dirty hack in place, introducing a boolean indicating it should send events or not, but that turned out to be insufficient.

1 minute read

CKAN 1.0: A major contribution to Open Knowledge

Peter informed about the CKAN 1.0 release. I browsed the 27 chemistry packages, and saw for example BODR show up:

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Cleaner CDK Code #5: develop against interfaces

Rajarshi is at the EBI (or at least was yesterday), talking about his rcdk package (his excellent slides). One slide is about how to create a new atom; he mentions not to use new Atom() but the DefaultChemObjectBuilder instead (slide 73). I do not entire agree with the message given.

2 minute read

Three ACS-RDF sessions

It has been a while since I gave an update on the ACS-RDF session in Boston. Things are settling in, and it seems there will be three sessions, each with an approximate theme. Each session will have five talks, of which one will be extended, where the speaker will be invited to set the context of the theme. Full programs will follow, but find the current sessions wordles below:

less than 1 minute read

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