Dear all,
The underlying RDKit libraries used in the RDKit KNIME nodes have been updated to version 2016.03.4. This is now available in the RDKit node nightly builds. The new overall version number for the nodes is 3.2.1 (it is a *pure* coincidence that this is the same as the KNME version number...).
The backend changes are all bug fixes. If you want to know what has changed relative to the 2016.03.2 release previously being used, the release notes are here: https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_3 and here: https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_4
In addition to the bug fixes provided by the backend updates, improvements have been made to the way 3D structures are generated in the RDKit nodes. The 3D generation code now by default uses the improved RDKit conformation generation described in tihs paper: http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00654 . There is also an overview in this presentation from last year's RDKit UGM: https://github.com/rdkit/UGM_2015/blob/master/Presentations/ETKDG.SereinaRiniker.pdf
Here's what that means to you:
- RDKit Generate Coords will now use the experimental torsion angle and "basic knowledge" terms discussed in the paper and presentation referenced above when you generate 3D coordinates.
- The RDKit Add Conformers node has, in the advanced tab, the ability to toggle the use of the experimental torsion and basic knowledge terms. These default to be turned on. The exception to this is that the results produced by workflows that already have an "RDKit Add Conformers" node will not change unless you manually change the settings on the advanced tab.
-greg