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The Chemistry Development Kit

@cdk.fosstodon.org.ap.brid.gy

Cheminformatics toolkit written in Java and started in September 2000, which can be used in Groovy, Python, and other languages too. [bridged from fosstodon.org/@cdk on the fediverse by fed.brid.gy ]

Posts Replies Media

The Chemistry Development Kit @cdk.fosstodon.org.ap.brid.gy · 18/08/2026

and hot on the heels, the CDK Scaffold extension had the 2.13 release too: 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.

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The Chemistry Development Kit @cdk.fosstodon.org.ap.brid.gy · 18/08/2026

CDK 2.13 was released: doi.org/10.5281/zenodo.21992083 - cdk-iordf now available separately - more SMIRKS - fragmenter for cicular substuctures - reaction centers in MDL V2000 - CXSMILES coordinate bonds - improved metal sandwich rendering Full […] [Original post on fosstodon.org]

2D renderings of ferrocene and uranocene. Both are a metal atom in the middle (iron and uranium), sandwiched between two organic aromatic rings.

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The Chemistry Development Kit @cdk.fosstodon.org.ap.brid.gy · 03/03/2026

CDK 2.12 was released: doi.org/10.5281/zenodo.18850648 The release notes are here: github.com/cdk/cdk/releases/tag/cdk… One new feature is support for atropisomers, see the screenshot #openscience #cheminformatics

CDK has supported atropisomers for some time but only via 2D coordinates with layouts and CIP naming etc working as expected. RDKit has an extension to allow loading from CXSMILES - although it is not perfect I was at a loss to think of something better and so it makes sense to support it. Currently this is read-only and mainly intended for depiction.

For example this CXSMILES:

C=CC(=O)N1CCN(c2nc(=O)n(-c3c(C)ccnc3C(C)C)c3nc(-c4c(O)cccc4F)c(F)cc23)[C@@H](C)C1 |wU:12.23| (m)-sotorasib

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The Chemistry Development Kit @cdk.fosstodon.org.ap.brid.gy · 11/09/2025

nice new R-group SMILES enumeration feature in the upcoming JChemPaint release, see github.com/JChemPaint/jchempaint/pu… #openscience #chemistry

Screenshot of a frame of one of the videos in the linked pull request, showing a chemical structure with various R-groups on the left (code and R group values), and on the right a list of SMILES combinatorial structures generated from the input on the left.

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The Chemistry Development Kit @cdk.fosstodon.org.ap.brid.gy · 20/04/2025

Impact of our articles (and part of that of our source code; not every citation is an article where the CDK is used), according to OpenAlex. About 75 citations per year, totalling to 1716. And note how often those articles are cited.

Screenshot of the link OpenAlex page, showing a query asking for all articles citing 5 articles (3 main articles, and 2 derivaties) and then the 4 most cited articles (citing the CDK) on the left, and some statistics on the right. These include the total citation sum (1,716), that 58.7% of the citing articles have been published open access, that they are mostly artices (1267), followed by preprints, reviews, book chapters, and dissertations (32). And that most citations come from the USA (380), followed by Germany (272), China (217), UK (210), and Switzerland (100).

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The Chemistry Development Kit @cdk.fosstodon.org.ap.brid.gy · 11/03/2025

a beta release of JChemPaint 3.4 is now out: github.com/JChemPaint/jchempaint/re… #CDK25UGM

Screenshot of JChemPaint with a SMILES with stereoinfo for the Pt for cis-platin and trans-platin

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The Chemistry Development Kit @cdk.fosstodon.org.ap.brid.gy · 04/03/2025

the main JChemPaint branch has been rebased on CDK 2.10 and contains many new improvements. This PR contains a few short videos with some of the changes: github.com/JChemPaint/jchempaint/pu… #chemistry

Screenshot of a still of one of the videos, showing an editing session in the JChemPaint 2D chemical editor, with a highlighted alkane chain attached to a phenyl ring, about the be rotated.

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