Announcing New Version of RDKit Nodes 4.12.0 / 5.2.0 for KNIME 5.1, 5.2 and 5.3

Community Extensions
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Dear KNIME RDKit Users,

we have just released a new version of the nightly build as official releases for KNIME 5.1, 5.2 and 5.3.

What has changed?

Improvements and Updates:

  1. New RDKit Binaries 2024.09.2: Information about detailed changes you can find here . We are aware of the following changes (discovered during our regression testing):
  • Wording of error message for molecule generation has changed slightly, including now more useful information in case of failures
  • Coordinate generation for molecules may lead to slightly changed results
  • Some new options are available now in the R Group Decomposition node: Added NoSymmetrization and GA as new Matching settings.
  1. Fixed Security Vulnerabilities Related to OPSIN integration
    We upgraded the commons-io library to the latest available and compatible version.
  2. Bugfix for avoiding crashes of RDKit when running the RDKit Molecule Highlighting node
    When running this node in highly parallel scenarios, in very rare cases users may have encountered a KNIME crash caused by the RDKit/Java integration. We found a way to workaround this issue - there are no crashes anymore.
  3. Bugfix for the Chemical Transformation Node
    We improved the handling of intermediate products in chemical transformations. Such products caused issues in some situations because they were not sanitized before being used further in the next transformation cycle. This has been changed now: They are now sanitized before they are re-used.

The update is available

  • for KNIME 5.1 and 5.2: RDKit Feature 4.12.0, and
  • for KNIME 5.3: RDKit Feature 5.2.0

Organizational Changes At Novartis
I would also like to take the opportunity to say Goodbye to this community. At Novartis we have had in summer 2024 some reorganizations, and as part of this I will work in a different role and will not be able to support the KNIME RDKit Extension any further. I have handed over responsibilities inside of our Novartis KNIME team to ensure continuity. You will be supported in the future by Stephen H. Johnson who took my role as Novartis KNIME Tech Lead. Thanks for 14 nice years of “kniming” together! And thanks for using RDKit!
I will be not completely gone, but turning more into a “regular” KNIME user. :slight_smile:

I wish you all nice year-end holidays!

Kind regards,
Manuel Schwarze

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