Saturday, May 11, 2013

Groovy Cheminformatics with the CDK - 8th edition

Update: I have uploaded the full ToC to FigShare.

It is still not what I want to release on as a final version, but fewer and fewer bits are, what I consider, missing. And with a whopping 228 pages I am happy I have a solid build system where I can just hack in new code and update the CDK version easily. In fact, this version adds 10 new scripts since the 7th edition. Some scripts take more time than others, and four of these are solutions I wrote for the Chemistry Toolkit Rosetta (CTR) by Andrew Dalke (see also this blog post).

There are two versions:
  1. paperback, for $ 45
  2. eBook, for $35, a PDF version
Still, this revision does not add that much new content:
  • Section 2.2.2. Bond stereochemistry (just refers to Chapter 3)
  • Chapter 3. Stereochemistry
  • Chapter 19. Chemitry Toolkit Rosetta
  • Section 21.3.2. Grabbing dependencies (for Groovy)
The start of the stereochemistry chapter is interesting, explaining wedge bonds and the ITetrahedralChirality interface, but obviously I have to add the IDoubleBondStereochemistry will have to follow soon.

The first words of Chapter 19 look like what I tumblred earlier today (yes, I have an introductory chapter upcoming but not ready yet, causing the chapter numbering to differ):

The CTR chapter has solutions of four of the challenges listed in the wiki. I have not yet managed to create solutions for all 18 of them, as intended.

I still like to stress that the book is for convenience: it only groups together information that you can find elsewhere as well. For example, the solutions to the four CTR problems can be found in that wiki too. The solution is there, and the explanation is in the book.