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Wednesday, December 26, 2018

Groovy Cheminformatics rises from the ashes

Cover of the last print
version of the book.
Like a phoenix (Phenix aegyptus), my Groovy Cheminformatics rises from the ashes. About a year ago I blogged that I could not longer maintain my book, not in the print form. The hardest part was actually resizing the cover each time the book got thicker. I actually started the book about 10 years ago, but the wish to make it Open Access grew bigger with the years.

So, here we go. It's based on CDK 2.0, but somewhere in the coming weeks I'll migrate to the latest version. It will take some weeks to migrate all content, and your chapter priority requests here.

The making of...
Over the past months I have been playing with some ideas on how to make the transition. I wanted to preserve the core concept of the book that all books are compiled and executed which each release and that all output of scripts is autogenerated (including many of the diagrams). I wanted to publish the next iteration of the book as Markdown, but also pondered with the idea of still being able to generate a PDF with LaTeX. That means I have a lot of stuff to upgrade.

I ended up somewhere in between. It's source is Markdown, but not entirely. It's source code that looks like Markdown with snippets of XML. This makes sure the source looks formatted when on GitHub:
But you can see that this is not processed yet. The CreateAtom1 and CreateAtom2 refers to code examples, and the above screenshot shows the source of a source code inclusion (for CreateAtom1 and CreateAtom2) and a output inclusion (for CreateAtom2). After processing, the actual page looks like this:


That looks pretty close to what the print book had. An extra here is that you can click (hard in a print book) the link to the code. That is something I improved on along the way, and leads to a Markdown (new) page that shows the full sources and the output (should I add the @Grab instructions, or too obvious?):


If you check the first online version (🎶 On the first day of xmas, #openscience got from me ... 🎶), I have quite some content to migrate. First, back to doing the reference sections properly, as if I was still working with BibLaTeX.

Happy holidays!