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Saturday, June 10, 2017

New paper: "The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching"

This paper was long overdue. But software papers are not easy to write, particularly not follow up papers. That actually seems a lot easier for databases. Moreover, we already publish too much. However, the scholarly community does not track software citations (data citations neither, but there seems to be a bit more momentum there; larger user group?). So, we need these kind of papers, and just a version, archived software release (e.g. on Zenodo) is not enough. But, there it is, the third CDK paper (doi:10.1186/s13321-017-0220-4). Fifth, if you include the two papers about ring finding, also describing CDK functionality.


Of course, I could detail what this paper has to offer, but let's not spoil the article. It's CC-BY so everyone can readily access it. You don't even need Sci-Hub (but are allowed for this paper; it's legal!).

A huge thanks to all co-authors, John's work as release manager and great performance improvements as well as code improvement, code clean up, etc, and all developers who are not co-author on this paper but contributed bigger or smaller patches over time (plz check the full AUTHOR list!). That list does not include the companies that have been supporting the project in kind, tho. Also huge thanks to all the users, particularly those who have used the CDK in downstream projects, many of which are listed in the introduction of the paper.

And, make sure to follow John Mayfield's blog with tons of good stuff.