chem-bla-ics: March 2010

Cleaner CDK Code #4: inheriting JavaDoc from super classes and interfaces

When you write a class implementing an interface or extending a super class, it is often the case that the API is identical. It would be nice to inherit the JavaDoc documentation, which is possible.

Inheriting JavaDoc

Java method that overwrite a superclass method or implement an interface method, can inherit JavaDoc by including this JavaDoc for that method:

/** {@inheritDoc} */ @TestMethod("testGetMIMEType") public String getMIMEType() { return null; }The JavaDoc documentation notes that missing @param and @return values are inherited implicitly since JavaDoc 1.3, but I have never noticed this in Java6. The above explicit markup is confirmed to work.

Mar

ACS Boston: RDF Symposium update

The deadline for abstract submission for the ACS symposium on Semantic Chemistry with the Resource Description Framework has passed. Eleven independent abstracts made the deadline. Here's what you can expect in Boston:

If you are new to Resource Description Framework and related technologies, I can recommend the book Programming the Semantic Web, which I read with pleasure.

Mar

CDK-Taverna paper published

It took a while, but the CDK-Taverna paper (doi:10.1186/1471-2105-11-159) which has been in preparation for a while in the CDK subversion repository, is now published. Christoph already wrote up a brief explanation in his blog:The workflow paradigm allows scientists to flexibly create generic workflows using different kinds of data sources, filters and algorithms, which can later be adapted to changing needs.

Mar

Updated my blog template

I noted today that blogger.com, the blog service provider I am using, had new templates. I was getting tired of the old one anyway, so tried the simple template using the usual orange: quite satisfactory! At least, beats buying a book like this Blogger: Beyond the Basics. Don't have time for that.

I tweaked the template a bit. For example, the default labels widget does not allow me to limit the shown labels to those with at least X uses.

Mar

Cleaner CDK Code #3: run the PMD tests

PMD is a tool to run some tests against your source code. The check for code style, common problems, and places where code could be improved. The CDK has been using it for years now, such as here for CDK 1.3.x.

Mar

Oxford, August 2010: eCheminfo Predictive ADME & Toxicology 2010 Workshop

The first week of August I will attend the eCheminfo Predictive ADME & Toxicology Workshop (LinkedIn Event) for which I received a Bursary Award. It will be my first time in Oxford, and I am very much looking forward to it!

The meeting is also bound to be fun. I have not done much in the area of toxicology other than the more general QSAR/QSPR model building with chemometrics.

Mar

Cleaner CDK Code #2: String.contains() and logger messages

Second in the series (see #1), with two rather small tips.

Use String.contains() instead of String.indexOf("foo") != -1

Java 5 introduced the method public boolean contains(CharSequence s), which can replace the more cryptic use of indexOf() != -1.

Mar

RDF-powered QSAR wizard: SPARQL end points providing wizard content

As you know from my blog, one of the things I am working on is to push RDF functionality in Bioclipse, as I believe it to be the missing link between molecular chemometrics and literature, databases, and other non-numerical information sources.

As part of the submission for the SWAT4LS special issue in the new Journal of Biomedical Semantics, Ola hacked up a cool wizard that sets up a new QSAR Project by downloading data directly from our RDF node for the chEMBL data using SPARQL.

Mar

Cleaner CDK Code #1: List and the for-each loop

In a desperate attempt to force me to write on my CDK code snippet book, I'm going to write some code tips to create clear code. Hopefully, this is useful for people writing patches and reviewers alike, too.

Use List instead of the untyped List

Quite some time ago, the Java language introduced typed lists. These lists can contain only objects of a particular type, which is a very common use case. Indeed, the CDK has quite a few lists that are strongly typed.

Mar

OOChemistry 0.1 released: call for participation

Konstantin released OOChemistry 0.1 and sent this email to the cdk-jchempaint mailing list (I added a few links and an extra newline):Hello, colleagues! I'd like to announce first alpha version of OOChemistry. It is an extension for OpenOffice.org which provides cross-platform OLE-like integration of OOo with JChemPaint chemical diagram editor.