RDKit Nodes 3.0.0 Released

[manuelschwarze]

Dear RDKit Nodes Users,

we have just released a new official RDKit Nodes version 3.0.0, which will be available in KNIME 3.1 coming Dec 6th 2015. It contains the following changes and improvements:

• General changes:

  <ul>
  	<li><strong>Updated RDKit Binaries to version&nbsp;2015_09_02:</strong>
  
  	<ul>
  		<li>MQN12 Descriptor Calculation changed (bugfixes)</li>
  		<li>SDF to Molecule code bugfix lets sanitization fail now for some bad molecules&nbsp;</li>
  		<li>Other changes in binaries are documented at http://www.rdkit.org</li>
  	</ul>
  	</li>
  	<li><strong>Many changes driven by architectural and API changes that came with KNIME 3.x:</strong>
  	<ul>
  		<li>Supports now for many RDKit Nodes input table sizes larger than 2 billion rows.</li>
  		<li>Instead of plain RDKit Molecule Cells&nbsp;we are creating now RDKit Adapter Cells that contain an RDKit Molecule Cell&nbsp;instance. This will lead to better workflow handling when using mixed chemical node sets.</li>
  		<li>Instead of Smiles Cells we are creating now Smiles Adapter Cells.</li>
  		<li>Instead of Sdf Cells we are creating now Sdf Adapter Cells.</li>
  		<li>Tons of internal changes that you hopefully will never notice. :-)</li>
  	</ul>
  	</li>
  	<li><strong>Major change in RDKit From Molecule Node:&nbsp;</strong>If the in-coming column to be converted supports multiple chemical formats, it will use an SDF format before a SMILES format now. Takes first into account what is directly available (isCompatible() check), and afterwards if something is adapted (isAdaptable() check).<br />
  	<br />
  	<u>Example:</u> An SDF Reader node produces an SDF column, which somebody uses directly with the RDKit Fingerprint Node. This generates fingerprints, but (without the user really knowing) it changes also the SDF input column and attaches auto-converted RDKit Molecule Cells, which can be used later on by other RDKit Nodes without doing the auto-conversion over and over again. As the RDKit Molecule Cell implementation serves also the RDKit converted SDF format, it is important now for the RDKit From Molecule node that the SDF input is being taken from the originating SDF column and not from the attached RDKit Molecule Cell. The user wants the original, not the auto-converted SDF.</li>
  	<li><strong>Removed old deprecated RDKit Molecule Cell implementation used in RDKit Nodes 1.0.0.</strong> This was not used for ages anymore, hence in our opinion there should not be any workflows that depend on that very first implementation of an RDKit Cell.</li>
  </ul>
  </li>
  <li>​<strong>Added new RDKit nodes:</strong>
  <ul>
  	<li><strong>​</strong>RDKit Molecule Extractor node:
  	<ul>
  		<li>Used to split-up disconnected fragments in a mol block. They could for instance be the result of molecule sketching done in the web portal of KNIME (commerical software) or with Marvin sketcher.</li>
  	</ul>
  	</li>
  </ul>
  </li>
  <li><strong>Bugfixes:</strong>
  <ul>
  	<li>RDKit Murcko Scaffold Node:
  	<ul>
  		<li>This node had the isotope&nbsp;value in the result molecules&nbsp;always set to 12. Now it is working correctly.</li>
  	</ul>
  	</li>
  	<li>RDKit Remove Hs node:
  	<ul>
  		<li>Sanitizes a molecule&nbsp;now after removing Hs so that RDKit 2D Depiction of the molecule works properly.</li>
  	</ul>
  	</li>
  </ul>
  </li>
  

Thanks to all users who were using and testing our nightly build version. We hope you all will enjoy these changes together with KNIME 3.x  --- Thanks for using RDKit in KNIME! Please report any bugs and strange behavior you may encounter to this RDKit Forum.

Kind regards,
Manuel