Chemistry Development Kit nodes for KNIME

New stable release of KNIME-CDK (v.1.4.1) now available.

• Dramatic speed up of node execution for all nodes.
• New node for highlighting molecule symmetry groups.
• New functionality to highlight found substructures for the Substructure Search node.
• New global option to show aromatic structures in Kekulé or Ring form.
• Improved I/O functionality.
• Improved visualisation of molecules.
• Revamped core architecture, now fully CML based.

Examples

Example workflows can be found under myExperiment or on the public KNIME server under "community/cdk".

About the nodes

These nodes have been developed in collaboration with the KNIME group. The nodes provide basic cheminformatics functionality to deal with molecular compounds. Currently the following features are available:

• Conversion of molecules to and from SDF, Mol2, Smiles and CML
• Sketching of molecular structures
• Calculation of 2D/3D coordinates
• Substructure search and substructure highlighting
• Molecule symmetry group calculation
• Signature and fingerprint generation
• Rendering of atom identifiers
• Visualisation of molecular structures in 3D space
• Calculation of fingerprints and Tanimoto distance/similarity
• Manipulation of explicit hydrogens
• Calculation of a range of molecular properties, XLogP and Lipinski's Rule of Five
• Structure connectivity testing

The CDK KNIME integration is under constant development. If you have any questions, bug-reports or suggestions for new nodes, please let us know in the CDK KNIME forum.

About the CDK

The Chemistry Development Kit design originated from a meeting on September 27-29 2000. Over the years, the CDK library was developed and evolved into a fully blown open source and open development chemoinformatics package with code reaching from QSAR descriptor calculations to 2D and 3D model building. 

For further information, please see the CDK Wiki or join the active user base by subscribing to one of the CDK mailing lists.

License

The CDK extension is released under LGPLv3.