Cleaner CDK Code #8: the Java Naming Conventions and Camel Casing

Another simple approach to make your code more readable, is to adhere to the Java naming conventions. They prescribe that variables start with a lower case characters, as do method names. Class and interfaces, however, start with upper case characters. By all using these same conventions, we need to learn only one scheme and can more easily recognize what are variables, methods and classes. Have a look at these naming conventions by Oracle and the concept of Camel Casing, heavily used in Java.

1 minute read

Oxford... #2

The Predictive Toxicology meeting is over. It was a great meeting, by any standard. Very much recommended, and many thanx to Barry for the organization! The meeting was a true workshop, with a mix of presentations and getting work done. I participated in a group that looked at mutagenicity of potential anti-malaria drugs from the datasets of GSK and Novartis recently release as Open Data. We used various tools to predict properties, and plan to make all our results freely available soon. Otherwise, it was also great to meet Nina again (with whom I talked about OpenTox), and to meet other CDK users, including Patrik (SMARTCyp , doi:10.1021/ml100016x) and David (Inkspot).

less than 1 minute read

Cleaner CDK Code #7: understand what the code is supposed to do

It has been a while since I posted a blog post in this series (see below for a full list so far), but was fixing a problem for Nina (OpenTox), and found some code I did not understand. So, here’s another useful tip (IMHO) for writing CDK code. Well, in particular, patching CDK code in this case.

3 minute read

Using Bioclipse to upload data to an OpenTox server

As part of a continuing mashup of Bioclipse and OpenTox, I sat down with Nina in Oxford to implement uploading molecules from within Bioclipse with JavaScript to OpenTox servers. This opens the route to calculate QSAR descriptors using the OpenTox API.

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Is there an Open Specification for structure normalization?

Over at the Blue Obelisk eXchange, I just posted this question:

less than 1 minute read

Oxford...

Yesterday, I arrived in Oxford, after a 3.5 hour bus transfer from London Stansted. Long, boring ride (though I might have seen a few red kites, but seeing that they were near extinct, I am wondering what other large bird of prey has strong split tail like a swallow). Showed once more that the UK infrastructure has hardly changed since the 19th century. Enjoying an undergraduate room at one of the colleges. Pretty basic, but makes me feel more like a human than a tourist. Yes!, undergraduate students are human too! One of the advantages is you get an excellent internet connection :)

2 minute read

CDK 1.2.6: the changes and the authors

Like all release in the 1.2 series after CDK 1.2.0, release 1.2.6 is a bug fix release. Anyone running a CDK 1.2 version is advised to upgrade. New in this release is the availability of a torrent for the cdk-1.2.6.jar (see BitTorrents for Science). Please find below the changes and the authors that contributed to this release.

5 minute read