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cdk.fosstodon.org.ap.brid.gy
The Chemistry Development Kit
@cdk.fosstodon.org.ap.brid.gy
15 followers 2 following 21 posts
Cheminformatics toolkit written in Java and started in September 2000, which can be used in Groovy, Python, and other languages too.

[bridged from https://fosstodon.org/@cdk on the fediverse by https://fed.brid.gy/ ]
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cdk.fosstodon.org.ap.brid.gy
and hot on the heels, the CDK Scaffold extension had the 2.13 release too: https://doi.org/10.5281/zenodo.22000770

Based on CDK 2.13 and with some notes on how it handles stereochemistry and a fix. See […]

[Original post on fosstodon.org]
Screenshot of the linked page about stereochemistry. It shows the "Version 2.13" section, with this text: "In the upcoming CDK and CDK-Scaffold release 2.13, this issue will be fixed. Then, all parent scaffolds will retain the correct stereoconfiguration as long as possible (all scaffold tree parent scaffolds are listed below):" And then shows 8 depictions to illustrate the new behavior.
August 18, 2026 at 8:15 PM
Reposted by The Chemistry Development Kit
egonw.social.edu.nl.ap.brid.gy
@[email protected] one things I learned about was the notion of "attachment points" in CXSMILES... works nicely in @wikidata :)

#cdk25ugm
Screenshot of a record of Wikidata of a (P31 = instance of) "functional group", showing a regular SMILES with a "[*]" and a CXSMILES with the same but the "CX" addition "$_AP1$" causing the CDK-depiction to show a wigly line perpendicular to the bond "attaching the functional group" to the rest of the molecule.
March 16, 2025 at 7:07 PM