RDKit Nodes for KNIME (trusted extension)

About the nodes

These nodes, developed in collaboration with KNIME, provide some basic, but robust and high-performance, chemistry functionality within KNIME. The current set of nodes includes functionality for:

  1. Converting between SMILES or SDF and RDKit molecules
  2. Generating canonical SMILES
  3. Substructure filtering using SMARTS or RDKit molecules
  4. Substructure counter with visualization of counted substructures
  5. Highlighting atoms in molecules for, for example, showing the results of substructure matching
  6. Filtering sets of molecules by presence or absence of well-defined functional groups.
  7. Chemical reaction enumeration
  8. Stripping off salts from molecules
  9. Picking diverse molecule subsets
  10. R-group decomposition
  11. Generating Murcko scaffolds and frameworks
  12. Generating 2D coordinates for molecules, optionally including a template.
  13. Generating 3D coordinates for molecules.
  14. Generating a variety of molecular fingerprints and reading and writing fingerprint files:
  • RDKit fingerprints (Daylight-like topological fingerprint)
  • Morgan fingerprints (ECFP/FCFP-like circular fingerprints)
  • Atom pairs
  • Topological torsions
  • Avalon fingerprints

We will be adding more nodes to the collection over time. If you have suggestions for nodes that should be added, please let us know either in the KNIME forum or on the RDKit-discuss mailing list.


Some example workflows can be found on the KNIME Public server that is accessible from within each KNIME installation (look for 099_Community/01_RDKit).

About the RDKit

The RDKit is an open-source cheminformatics toolkit written in C++ that is also useable from Java or Python. It includes a collection of standard cheminformatics functionality for molecule I/O, substructure searching, chemical reactions, coordinate generation (2D or 3D), fingerprinting, etc. as well as a high-performance database cartridge for working with molecules using the PostgreSQL database. The toolkit is covered by the BSD license.

More information about the RDKit is available from the website www.rdkit.org.

Source Code

The source code can be accessed at https://anonymous:knime@community.knime.org/svn/nodes4knime/trunk/org.rdkit.


The RDKit nodes are released under GPLv3.


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