Rogue Scholar Beiträge

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Veröffentlicht in chem-bla-ics

In the CDK2024 grant we wrote about updating various software projects using the Chemistry Development Kit. We even wrote that “[r]equired API changes will be publicly shared and disseminated with the Groovy Cheminformatics with the Chemistry Development Kit book (egonw.github.io/cdkbook/)”. The Groovy Cheminformatics with the Chemistry Development Kit book is a project that has run since 2009.

Veröffentlicht in chem-bla-ics

Publishing grant proposal is still not very common. The proposal published in Research Ideas and Outcomes) (doi:10.3897/rio.10.e124884) for the NWO Open Science grant for the CDK is, however, not the first and hopefully not the last. Interestingly, it is already cited in (the German) Wikipedia. It is used there to support a statement which tools use the Chemistry Development Kit.

Veröffentlicht in chem-bla-ics

We recently got awarded our second NWO Open Science grant (OSF23.2.097), this time for the Chemistry Development Kit (CDK). “We” here is me and Alyanne de Haan, René van der Ploeg, and Marc Teunis from Hogeschool Utrecht. The proposal has been submitted for public dissemination in RIO Journal, like we did with the first NWO Open Science grant.

CdkChemieEnglisch
Veröffentlicht in chem-bla-ics

I cannot find the bug report just now, but the CDK has an open problem with change even notification, where the nonotify classes still caused change event to be sent around. This was because the nonotify classes extended in a wrong way the data classes. So, I worked today on copying the data class implementations into a new implementation, not extending the data classes, while removing the listener code: the silent module.

Veröffentlicht in chem-bla-ics

Last month I reported a few things I missed in CiteULike. One of them was support for CiTO (see doi:https://doi.org/10.1186/2041-1480-1-S1-S6), a great Citation Typing Ontology. I promised the CiTO author, David, my use cases, but have been horribly busy in the past few weeks with my new position, wrapping up my past position, and thinking on my position after Cambridge.

Veröffentlicht in chem-bla-ics

The Predictive Toxicology meeting is over. It was a great meeting, by any standard. Very much recommended, and many thanx to Barry for the organization! The meeting was a true workshop, with a mix of presentations and getting work done. I participated in a group that looked at mutagenicity of potential anti-malaria drugs from the datasets of GSK and Novartis recently release as Open Data.

Veröffentlicht in chem-bla-ics

Day 5 was formally the last day (see also the summaries of day 1, day 2 and day 3/4) of the Chemistry Development Kit Bug Squash Party (BSP). Miguel uploaded the last bits of his CDK PDBPolymer to CML to CDK PDBPolymer roundtripping functionality (closing a bug and a feature request in one go). Have not tested this first hand yet, but looking forward to playing with this bit of code.

Veröffentlicht in chem-bla-ics

Because I was struggling hard with default values for cdk.interfaces fields, I did not have time to write up the Bug Squash Party report for day 3 (see also day 1 and day 2). But here it is. Day 3 Kai worked hard on getting the cdk.interfaces API cleaned up, as agreed upon earlier. Christian added a test for the RMSD calculator (see getAllAtomRMSD()), and cleaned up his code a bit.