Dear RDKit Nodes Users,
we have just released a new official RDKit Nodes version 2.5.0, which is available for KNIME 2.11 (and soon in KNIME 2.12). It contains the following changes and improvements:
<ul> <li>Updated RDKit Binaries to version 2015_03_1. This is a major change and updates the algorithms how SMILES are canonicalized! Please re-execute intermediate results which are based on canonicalized SMILES.</li> <li>Python integration. RDKit column types integrate now nicely with KNIME’s Python Nodes that allow to run RDKit also in Python and exchange molecule and fingerprint based data.</li> <li>Added MCS aggregation functionality that will show up in KNIME's GroupBy node.</li> <li>Improved GUI in node dialogs.</li> <li>Improved documentation.</li> </ul> </li> <li><strong>Deprecated RDKit nodes:</strong> <ul> <li>RDKit Highlighting Atoms node (there is a much better one added instead)</li> </ul> </li> <li><strong>Added new RDKit nodes:</strong> <ul> <li>RDKit Structure Normalizer node, which is based on StruChk, an Avalon component part of the RDKit</li> <li>RDKit MCS node</li> <li>RDKit Count-based Fingerprint Node</li> <li>RDKit Highlighting node, which offers more sophisticated highlighting of atoms and also bonds</li> </ul> </li> <li><strong>Improved the following RDKit nodes:</strong> <ul> <li>RDKit From Molecule: <ul> <li>Added new TreatAsQuery option</li> </ul> </li> <li>RDKit Optimize Geometry: <ul> <li>Supports now switching off optimization to just calculate the energy of an existing molecule conformation</li> </ul> </li> </ul> </li> <li><strong>Bug fixes:</strong> <ul> <li>RDKit Substructure Filter: <ul> <li>Fixed bug in atom list generation used for atom highlighting, which contained always the 0 atom</li> </ul> </li> </ul> </li> <li><strong>Techie Stuff:</strong> <ul> <li>Bugfixes in RDKit Nodes Wizard templates that make a new RDKit node work with RDKit adapter cells.</li> <li>Made entire code base Java 1.7 compliant (no Java 1.6 support anymore)</li> </ul> </li>
A big Thank You to all users who were using and testing our nightly build version in the past, which accumulated these changes for quite some time now.
We hope you all will enjoy these changes --- Thanks for using RDKit in KNIME!