RDKit Nodes 2.4.0 Released

[manuelschwarze]

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 &quot;RDKit&quot;</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

[SOH979]

I can't see any description for rdkit pattern fingerprints, either in Knime or in RDKit - where are these described?

Cheers,

Steve.

[greglandrum]

Hi Steve,

There isn't really much of an explanation of how the RDKit Pattern fingerprint is generated. That's something I really should do, but just haven't managed to make time for.

-greg