I am happy to inform you that we’ve just released the KNIME RDKit nodes, version 4.6.0. The release should be available for versions 4.2, 4.3, 4.4, and 4.5 of the KNIME Analytics Platform.
For KNIME 4.6 we will release a version 4.6.1 with minor delay as it requires some additional adaptions. Expected for Wednesday, Dec 7, 2022.
For KNIME 4.7 there will be even more adaptions and exciting changes that @chaubold and @steffen_KNIME implemented. Stay tuned for more information about KNIME 4.7 features in connection with the RDKit nodes coming soon.
Changes in the release 4.6:
- The RDKit binaries have been updated to v2022.09.2 (this is the most recent release of the RDKit). Please be aware that SMILES canonicalization has changed in some cases, which may require a recalculation of existing data. A full list of changes can be found via Releases · rdkit/rdkit (github.com)
- The RDKit 2D Depiction renderer has been refactored to render SVG that make better use of existing space. Kudos to Paolo Tosco (@ptosco) for tuning RDKit binaries and helping with improvements.
- The RDKit 2D Depiction renderer supports now an individual configuration that can be performed by users or also on corporate level (via KNIME configuration). It gets configured via KNIME Preferences, menu KNIME - RDKit - RDKit 2D Depiction and takes a JSON structure of settings, which can be provided either from a file or directly in a text field.
- The “RDKit Molecule to SVG” node has been changed slightly to support fine granular bond lines, which are now set as Double instead of Integer value.
- The opsin library used in the “RDKit From IUPAC” node has been updated to fix a security vulnerability in library com.fasterxml.woodstox (CVE-2022-40152)
Many thanks to RDKit folks (@greglandrum, @ptosco and many others), and KNIME folks (@chaubold, @steffen_KNIME and @gab1one), who contributed to this release.
I just pushed an update of the RDKit feature with RDKit binaries 2022.09.3 (some bugfixes) and two improvements for working with RDKit in KNIME:
Support for normalizing structures during rendering: When rendering SDF / Mol Blocks their origin varies. Some tools use a different scale for the coordinates of a molecule, which causes sometimes atom labels with way too large fonts in the rendered molecule. We now allow to select in the preferences of RDKit 2D Depiction a normalization option to make the RDKit 2D Depiction of the molecule look always nice and consistent. By default this option is switched off.
Allow more tolerance when parsing SDF / Mol Blocks: There are several tools to sketch molecules. Sometimes, there are certain violations of the official standard introduced by these tools, and RDKit by default is very strict in parsing those structures. Hence, users run from time to time into failures. There is a flag in RDKit methods that allows to control how strict the parsing should be done.
We will influence this now in the following scenarios:
Auto-conversion: All RDKit nodes automatically turn SMILES or SDF structures into RDKit molecules. We added now a preference about strict parsing handling for this case. Default is true to be backward-compatible.
Rendering: The RDKit 2D Depiction rendering takes also plain SDF values and renders them after conversion into RDKit molecules. We added now a preference about strict parsing handling for this case. Default is false to have less failures in renderings.
Node Settings: Currently only 2 nodes could make use of the strict parsing setting: The “RDKit from Molecule” node (for converting SDF molecules) and the “RDKit R Group Decomposition” node (for reading cores in SDF format). We added now a node setting to control strict parsing. The default for old existing nodes will always be true. For new nodes the default is now controlled by a preference about strict parsing handling for this case. Default is true to be backward-compatible. In any case the user should be able to control the setting within the node settings. As it makes only sense for handling SDF we disable the setting for all other molecule types.
The update is available
- for KNIME 4.2, 4.3, 4.4, 4.5 as RDKit Feature 4.6.0,
- for KNIME 4.6 as RDKit Feature 4.6.1, and
- for KNIME 4.7 and in the nightly build as RDKit Feature 4.7.0.
We kept the same main version number as the update from early December (only the timestamp is newer), because we consider it a minor bugfix release with just some backward-compatible improvements.
Thanks to @ptosco and @greglandrum for their contributions! We wish all of you a Merry Christmas and a Happy New Year!
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