Dear RDKit Nodes Users,
we have just released a new official RDKit Nodes version 2.4.0, which is available for KNIME 2.8 and 2.9. It contains the following changes and improvements:
-
General changes:
<ul> <li>Updated RDKit Binaries to latest version</li> <li>Reorganized RDKit menu structure introducing sub categories</li> <li>Renamed a few conversion nodes - all nodes start now with the term "RDKit"</li> </ul> </li> <li><strong>Added new RDKit nodes:</strong> <ul> <li>Add Hs</li> <li>Remove Hs</li> <li>Aromatize</li> <li>Kekulize</li> <li>Add Conformers</li> <li>RMSD Filter</li> <li>Calculate Charges (Gasteiger charges)</li> <li>SDF Difference Checker</li> </ul> </li> <li><strong>Improved the following RDKit nodes:</strong> <ul> <li>Fingerprint: <ul> <li>Added Pattern fingerprint</li> <li>New parameters available for Torsion (path length) and AtomPair fingerprints (min, max path)</li> <li>Introduced rooted fingerprints as advanced option for most fingerprint types</li> </ul> </li> <li>Add Coordinates, Optimize Geometry, Open 3D Alignment: <ul> <li>Improved performance with parallel processing (multi-threading)</li> </ul> </li> </ul> </li> <li><strong>Bug fixes:</strong> <ul> <li>Auto-conversion of SMILES and SDF columns to RDKit Mol columns (RDKit Adapter Cell): <ul> <li>The original SDF or SMILES value will be maintained and used if SDF or SMILES values are used</li> <li>Copy and paste from RDKit Adapter Cell works now - it will use the SDF value if an SDF value was converted before, or the SMILES value, if a SMILES value was converted before</li> <li>Molecule type cast behavior has been fixed</li> <li>Auto-conversion of SDF cells with zero atoms to RDKit Molecules works now</li> <li>Auto-conversion of SMILES cells with empty strings to RDKit Molecules fails now with meaningful error message</li> </ul> </li> <li>Corrected auto-suggestion behavior for all nodes: Primarily RDKit Mol columns will be used, secondary SDF and tertiary SMILES</li> <li>Salt Stripper Node: A connected second table with SMARTS values will lead to the correct warning now that it cannot be processed but needs to be converted manually into an RDKit Molecule first</li> <li>Optimize Geometry Node: Fixed out of memory issue</li> </ul> </li>
We hope you will enjoy these changes! See you at the KNIME UGM in Zurich!
Kind regards,
Manuel