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The Chemistry Development Kit (CDK) @the_cdk

And open source library for bio- and cheminformatics. Mastodon: fosstodon.org/@cdk

Joined March 2015
  • Tweets 194
  • Following 8
  • Followers 570
24 Photos and videos
you can also follow us on #mastodon at fosstodon.org/@cdk

The Chemistry Development Kit (@cdk@fosstodon.org)

57 Posts, 8 Following, 49 Followers · Cheminformatics toolkit written in Java and started in September 2000, which can be used in Groovy, Python, and other languages too.

fosstodon.org
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The Chemistry Development Kit (CDK) retweeted
John Mayfield@jwmay
22 Aug 2023
The ChemistryDevelopmentKit (CDK) Java chemistry toolkits v2.9 is out! - More reaction arrow types - Multi-step Reaction SMILES extension/depiction - Universal (InChI) SMILES for large molecules - Better abbreviations #cheminformatics #CDK #Java Info: github.com/cdk/cdk/releases/…
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Last year, @csteinbeck's team published "Scaffold Generator: a Java library implementing molecular scaffold functionalities in the [... CDK]" doi.org/10.1186/s13321-022-0… Over the past year we have modularized it and the SNAPSHOT is now usable in Maven: s01.oss.sonatype.org/content…
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The Chemistry Development Kit (CDK) retweeted
ELIXIR Europe@ELIXIREurope
26 May 2023
🧬 Today’s #ELIXIRFridayReads is a @FAIRplus_eu, funded by @IHIEurope, paper focusing on the #FAIRCookbook 🧑‍🍳 - an online resource for “FAIR doers” in the #LifeSciences 🔑 Read more: doi.org/10.1038/s41597-023-0…
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The Chemistry Development Kit (CDK) retweeted
رامي عبدالله@RamiManaf
23 Feb 2023
Just finished developing JMolecularEnergy the first open source library for calculating MMFF94 force field in java! you can load molecules using @the_cdk and calculate their potential energy or minimize it.Check it out here ramimanaf.github.io/JMolecul… #chemoinformatics #java #rdkit
minocycline energy minimization

ALT minocycline energy minimization
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The Chemistry Development Kit (CDK) retweeted
John Mayfield@jwmay
3 Nov 2022
Arrow display now live on @cdk depict (dev). You can change the default with a drop down box or use a Data-Sgroup (via CXSMILES) to specify it.
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The Chemistry Development Kit (CDK) retweeted
John Mayfield@jwmay
3 Nov 2022
Fun quick patch last night, additional reaction arrow types: github.com/cdk/cdk/pull/927. Now to work out how to get these into to CDK depict
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if you like the CDK, plz star it on GitHub: github.com/cdk/cdk/stargazer…
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there is a pull request for SMIRKS support. Plz have a look at the functionality, API, and give us your feedback github.com/cdk/cdk/pull/916
Screenshot of the linked page showing two ways to use the API

ALT Screenshot of the linked page showing two ways to use the API
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CDK 2.8 is out! github.com/cdk/cdk/releases/…

Release CDK 2.8 · cdk/cdk

Key Changes JDK Versions: JDK 8 (minimum) JDK 11 (minimum if not using cdk-iordf) JDK 17 (recommended) The project is now built with Java 11 but compiled to target Java 8. If you have any issu...

github.com
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the next time you visit github.com/cdk/cdk you may see the a popup dialog. we changed the name of the default branch of 'main':
Screenshot of the link pages with a dialog telling: "The default branch has been renamed! master is now named main If you have a local clone, you can update it by running the following commands." and then showing the git commands to run

ALT Screenshot of the link pages with a dialog telling: "The default branch has been renamed! master is now named main If you have a local clone, you can update it by running the following commands." and then showing the git commands to run
just fyi, there is a lot happening right now. There are people working on CDK in AMBIT, CDK in KNIME, and integration of new functionality into the CDK.
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new chemfp release (includes the CDK): chemfp.readthedocs.io/en/lat…
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"As CDK is Java-based, its classes are accessed in Python via JPype [19]." jcheminf.biomedcentral.com/a…

RanDepict: Random chemical structure depiction generator

Journal of Cheminformatics - The development of deep learning-based optical chemical structure recognition (OCSR) systems has led to a need for datasets of chemical structure depictions. The...

link.springer.com
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we just had our 20 year anniversary (a bit delayed). At the start people wondered seriously about the sustainability. After two decades we can safely say, yes, #openscience also works in #cheminformatics github.com/cdk/cdk/graphs/co…
Twenty years, more than 100 contributors, and alive and kicking.

ALT Twenty years, more than 100 contributors, and alive and kicking.
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The Chemistry Development Kit (CDK) retweeted
Kohulan.R@KohulanRajan
5 Apr 2022
Continuing with the implementations of CDK over the past years @ESchymanski #cdk20y
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The Chemistry Development Kit (CDK) retweeted
Kohulan.R@KohulanRajan
5 Apr 2022
The history of CDK pubs.acs.org/doi/10.1021/ci0… eurekaselect.com/article/120… doi.org/10.1186/s13321-017-0… #OpenScience #OpenSource #cdk20y
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"SonarCloud found a bug in a 37 year old paper :-)" #PeerReview github.com/cdk/cdk/pull/843#…
"I will tag these ones as "won't fix" or will comment since it exactly replicates the original paper. So SonarCloud (and IntelliJ warns on it also) found a bug in a 37 year old paper :-)"

ALT "I will tag these ones as "won't fix" or will comment since it exactly replicates the original paper. So SonarCloud (and IntelliJ warns on it also) found a bug in a 37 year old paper :-)"

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The Chemistry Development Kit (CDK) retweeted
dalkescientific@dalkescientific
18 Feb 2022
Do people use chemfp's @the_cdk support? It's part of the standard chemfp installation. No license key needed. Here's a taste of chemfp 4.0's new cross-cheminf. toolkit API to read molecules and generate fingerprints. Or, replace "cdk" with "rdkit", "openbabel", or "openeye".
An example of using chemfp 4.0's new API for working with cheminformatics toolkits. It shows creating a 128-bit "Daylight" fingerprint for phenol, reading a small SMILES file to create an arena of CDK-Daylight fingerprints, and searching for the 3 nearest fingerprints for a query; displaying the results in Pandas.

ALT An example of using chemfp 4.0's new API for working with cheminformatics toolkits. It shows creating a 128-bit "Daylight" fingerprint for phenol, reading a small SMILES file to create an arena of CDK-Daylight fingerprints, and searching for the 3 nearest fingerprints for a query; displaying the results in Pandas.

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