Monday, June 06, 2011

Groovy Cheminformatics 2nd edition soon

In February I released the first edition of my book about writing cheminformatics software in the Groovy language using the CDK. The booklet was thinner than I expected for 72 pages (thin paper), which made the booklet look relatively expensive. Then again, it's not particularly making me rich. As explained before, I hope this will become a source of funding for continued CDK development. Anyways, today I worked hard to address some flaws in the first edition, and making some further tweaks.

The overall experience should be improved: I am now using the geometry package which should address the lack of whitespace near the top of each page, thanx to Jason Brownlee. I also noted that the bibliography styles abbrev and unsrt cannot be combined, and because this TeX StackExchange answer mentioned biblatex which I read about several times now, I decided it was time to dive in. I haven't gone the full biber route yet, and still using the CiteULike group for this book. I also hacked up automatic wrapping of output from the Groovy scripts in the book, which should further clean up the design. I doubt it is up to Jonathan's standards yet, but it will have to do for now.

On the content side, there are also interesting changes, and in particular the new sections and chapters. Per request, a list of all people who contributed to the CDK is added, as well as an overview of all CDK atom types. New material includes a short discussion on the IRing interface, a chapter on the InChI, words about generating tautomers (thanx to Mark for this new code!), examples on how to calculate various graph matrices, molecular formula, and how to calculate XLogP and TPSA properties.

All in all, the booklet now sums up to 104 pages, whereas the first version had 72. But, it's much too late already, and the alarm goes way too early in the morning, so the new edition will not appear online today.

Oh, and thanx to all who bought a copy of the first edition!


  1. I can highly recommend the memoir class [1]. I have been using it for a while and I love it.


  2. I am not seeking getting every pixel right, and I am not sure what memoir has to offer additionally. The content matters to me much more than getting the last layout details right. The second edition already does things better then the first, and when the book starts becoming part of cheminformatics curricula, then I'll start worrying about these things. (And I'll contact you then for consultancy :)

    In fact, I first need to get 2D depiction online, for which I first need CDK-JChemPaint to work :) The 3rd edition should have a chapter on 2D depiction.