RDKit Nodes 3.0.0 Beta Available Now For KNIME 3.0

Dear All,

since November 13, 2015, you can now install the RDKit Plugins 3.0.0 for the new version KNIME 3.0. It is still in beta state. Please give it a shoot and test it with your workflows. 

The following changes have been done. The main changes are really around molecule cell handling for input and output of chemistry nodes. The design and architecture in KNIME has changed to improve the collaboration between different types of chemistry plugins and the KNIME internal chemistry nodes, and the RDKit implements now the official guidelines using the so-called "AdapterCell" mechanisms.

  • Implemented changes for KNIME 3.0 (Eclipse 4.5, Java 8) according to the guidelines: https://tech.knime.org/api-changes-in-knime-30
    • Changed execution environment to JavaSE-1.8
    • KNIME 3.0 Dependency Declaration in Manifest files.
    • Row count allows now most tables to be larger than Integer.MAX_VALUE rows.
    • Extension point for data types is used now for RDKit cell types.
    • Comparing DataCells works now also on preferred value implementation.
    • Extension point for port types are used now when setting up node models.
    • Node extension points now implemented for all formerly deprecated RDKit nodes and set the attribute deprecated="true".
    • Changed deprecated Row Filter class of in RDKit Interactive Table to use the new Abstract Row Filter implementation that supports large tables.
    • AdapterCell related changes for KNIME 3.0:
      • Instead of RDKitMolCell2 we are creating now RDKitAdapterCells that contain an RDKitMolCell2 instance
      • Instead of SmilesCells we are creating now SmilesAdapterCells
      • Instead of SdfCells we are creating now SdfAdapterCells
      • Complete rewrite of the RDKitTypeConverter class for auto-conversion of SMILES and SDF input columns.
      • Changes also adapted in RDKit Node Wizard templates and sample code
      • Adapted Python RDKit Mol Deserializer to produce now RDKitAdapterCells.
  • Internal changes to make plugin compatible with Eclipse 4.5 APIs which is the base for KNIME 3.0. 
  • Improved RDKit Molecule memory cleanup mechanism to support large tables.
  • Removed old deprecated RDKitMolCell class.
  • Bugfix for RDKit Remove Hs node: Sanitizes molecule now after removing Hs so that RDKit 2D Depiction of the molecule works again.

Please report any bugs you may find back to us in this forum. Thanks for using RDKit!

Kind regards,

Manuel Schwarze