So, this new edition is again thicker, summing up to 152 pages now, which is 28 pages more than the 3rd edition . Indeed, the table of contents is more than half a page longer in itself, though, just barely, still fitting on four pages. In fact, I had to remove one (new) subsection title, because it would take otherwise two further pages.

The new content is again a mix of sections and chapters. While writing new chapters, I find myself realizing I need to cover more basics. Those get typically added as new sections. I did not get many feature requests, except for one email pointing me the text promised how to interpret and handle failing atom type perception, which explains one of the new sections. The full list of new content is:

• Section 2.1.4: explaining the three flavors of atomic coordinates
• Extended Section 2.2: added detail about electron counts of bonds (partly in reply to this post by Rich)
• Chapter 5 “Protein and DNA”: four pages, mostly about PDB files, and the matching CDK data structure
• Chapter 6 “IChemObjectBuilders”: four pages explaining the four alternative builders CDK 1.4.7 has
• Section 7.8: a new section with recipes on how to post-process read input, discussing MDL molfiles only now. It talks about what information is present in the file format, and what steps must be untertaken to add missing information
• Section 8.2.4 “No atom type perceived?!”
• Section 11.4: describes how to depict aromatic rings
• Section 11.5: describes how to change the background color of depictions
• Section 13.4: explains how to calculate the Van der Waals volume of molecules
• Section 18.1.3: discussing the API improvement in the iterating readers
• Appendix C: a list of all descriptors provided by the CDK
• Appendix D: a list of file formats known by the CDK, indicating which has readers and writers

On top of that, I improved other bits of the book too, such as the resolution of the depictions of molecules, as well as those of various diagrams. Also the number of scripts has seriously gone up, from 94 to 134!

Appendix C is a prelude to a chapter I am already writing, but did not get finished yet: a chapter about descriptor calculation. But since I just started a new post-doc position, it may take another six months for that chapter to make it into print.

The paperbak is available from Lulu.com, an on-demand publisher, as well as this ebook version.

I am starting to get the hang of this publishing soon, publishing often thing, and just uploaded edition 1.4.1-0 of the Groovy Cheminformatics book. The cover is the same (with one typo fix), and the content is 20 pages thicker. True, six of those pages are isotope masses of all natural isotopes. That leaves 14 pages with this new content:

• Section 2.7 on line notations with 2.7.1 about reading and writing SMILES
• Section 6.3 about Sybyl (mol2) atom types
• Section 7.4 on atom numbering with 7.4.1 on Morgan atom numbers, and 7.4.2 on InChI atom numbers
• Chapter 9 on molecule depiction with the new rendering code, with
  • Section 9.1 on drawing molecules,
  • Section 9.2 on rendering parameters, and
  • Section 9.3 on the generator API and how to add custom content
• Section 11.4 on calculating aromaticity
• Appendix A.2 listing all Sybyl atom types
• Appendix B listing all naturally occurring isotopes

Features requests most welcome.

Some project are never finished. Neither is this one, but it is never too late to change how things work, so, taking advantage of publishing-on-demand, here I introduce the release-soon, release-often equivalent of cheminformatics books, my Groovy Cheminformatics with the Chemistry Development Kit book:

With a serious discount for just being the first edition (1.3.8-0), but still counting at 72 pages with 75 code examples, this edition marks a personal milestone (and probably not much more than that). There remains much to do, but I promised a release by tomorrow, so here it is. Next releases will contain more code examples, more functionality descriptions, and more literature reviewing where such code is used in science. The plan is to make new editions with each new CDK release, as well as new editions when I added a new chapter, section, or just paragraph. But, there will not be a Nightly build service anytime soon.

The current table of content is as follows:

Now, the book content is not open content. However, it contains nothing that is not available in other means. It’s just the compilation that makes this book interesting, as well as that I put effort in ensuring the code examples remain working. For that, I ask a minor financial contribution.

CDK Keyword List by Egon Willighagen

And here about Groovy, which indeed is groovy:

Groovy CDK by Egon Willighagen

Clearly, any such documentation becomes quickly outdated, in particular when source code fragments are involved. Yes, CDK 1.2 is API stable, but only for the core classes. Moreover, I hope that the documentation will survive CDK 1.4 or 2.0 or whatever the next stable version is.

Therefore, I need to source code fragments compilable. R has the magnificent Sweave, and I wanted for a long time something similar. While I do not have something that powerful yet, at least my current set up allows me have code that both compiles and embeds in the LaTeX. The system allows me to write both Java application code as BeanShell scripts. No clue yet what I will use in the workshop, maybe even both. Like Sweave, it even saves output, and I can include that in the LaTeX source too. The code fragments can either go in as a verbatim section, or as a listing, depending on what I find more appropriate.