CDK iordf module. Contribute to cdk/cdk-iordf development by creating an account on GitHub.

Angehängt: 1 Bild BChemXtract - a ChemDraw parser and structure extractor - is our first open source software project and is available on @github@hachyderm.io: 🔗 https://github.com/Beilstein-Institut/BChemXtract #openscience #opensource #FAIRdata #FAIRchemistry #cheminformatics #GitHub #BeilsteinCheminfoLabs #BChemXtract

Twenty five years ago the Chemistry Development Kit (CDK) was founded. The Chemistry and Internet (ChemInt2000) had just ended (it ran from 23 to 26 September) and my friend and I had taken the Amtrak night train from Washington to South Bend. At that time there were two leading Java applets for chemistry, JChemPaint and Jmol. I had hacked Chemical Markup Language support into both of them, and Dan Gezelter (Jmol and openscience.org), Christoph Steinbeck (JChemPaint), and me took the opportunity of being in North America to discuss if we could use a common code base. Chris’ _compchem_ had done something similar. Peter Murray-Rust, who had also attended ChemInt2000 like me and Chris did not attend. I do not remember exactly, but I guess we must have met on the 28th and 29th? Maybe already on Wednesday. During this meeting we discussed a common data model (yes, Jmol used the CDK data model at some point) and somewhere during the meeting we wrote down a name for the project. There was the Java Development Kit, so this could be the Chemistry Development Kit. The name stuck. A quick post like this cannot do credit to the history of the CDK, nor of everyone involved in the past or still is. You can browse some of the history of the CDK in my blog and in Chris’ blog. It has been an amazing journey and with a small grant just behind us (with Alyanne de Haan, René van der Ploeg, and Marc Teunis from Hogeschool Utrecht), and all the awesome things ongoing (new JChemPaint, various extensions, upgraded downstream tools), the CDK is alive and kicking. A huge congrats and thanks to everyone (and every company and organization) who contributed code to the CDK with this huge milestone. There are a few people that I want to particularly thank (see the AUTHORS file for all names): Chris, who in the late nineties made a difference with open source in chemistry, Dan, for Jmol and hosting this memorable meeting at Notre Dame University, Rajarshi Guha, who operated _CDK Nightly_ for many years, well before Travis and Google Actions, Stefan, Miguel, Gilleain, and Christian, for many years of contributions to the CDK, and John Mayfield, the current CDK release manager.

Interim release fixing an issue in CDK 2.10.

Where the first workshop day had several talks about new and old features of the Chemistry Development Kit (CDK), the second day was a hackathon day. We hacked and we talked. The coding was not mostly only the CDK repository itself, but some things happened there too: Some pointers: * we worked on the Groovy Cheminformatics with the Chemistry Development Kit book * move the repository to the GitHub organisation * improved the build system * it was explored how the CDK can generate SMILES for glycans * continued work on updated tools using the CDK, e.g. ChemViz2 * code clean up, e.g. on JavaDoc and the XML parsing * a JChemPaint release, based on CDK 2.10, with a flatpak for easy install on many Linux distributions We further had discussions about a possible change of the license (what it would involve) and OSGi support. The problem there is that Java packages can only exist in one OSGi bundle, and this is currently not the discuss. We discussed that the current modules were partially setup to clean up dependencies, and generally modularize the CDK (e.g. each module could have a separate person responsible). We now want to propose a larger `core` module which covers the common cheminformatics functionality. A final discussion point I want to mention is that there are serious hints that we may have the Chemistry Development Kit as JavaScript in the browser soon! I like to thank every one who joined the workshop, particularly those that travelled to Maastricht from the UK, Germany, and Bulgaria. Also thanks to the six participants online who joined on the first day!

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Repository to track the progress of the NWO Open Science Grant accepted for the CDK in 2023.

A Java library that support various operations in force fields

The Chemistry Development Kit, for Java and JavaScript - BobHanson/cdk-SwingJS