RDKit nodes for KNIME

About the nodes

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

1. Converting between SMILES or SDF and RDKit molecules
2. Substructure filtering using SMARTS
3. Chemical reaction enumeration
4. Generating 2D coordinates for molecules, optionally including a template.
5. Generating 3D coordinates for molecules.
6. Generating a variety of molecular fingerprints:
   • RDKit fingerprints (Daylight-like topological fingerprint)
   • Morgan fingerprints (ECFP-like circular fingerprints)
   • Atom pairs
   • Topological torsions

We will be adding adding additional 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.

Examples

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.