Since May 2011, GGA Software Services provides Indigo-powered cheminformatics nodes nodes for KNIME. The overview of the nodes is available at KNIME Tech.
Installation
Prerequisities
First, you need to add the KNIME update site into your "software sites" list, if it is not already there (instructions). From that site, you need to download the Base Chemistry Types & Nodes (needed for the Indigo nodes to work) and the Distance Matrix (needed for one of the provided Indigo examples to work).
Indigo Nodes
You need to add the KNIME's Community Contributions Nightly Updates site to tour "software sites" list (instructions). Then, you need to download the "Indigo KNIME Integration" package.
"Unsigned Content" warning during the installation is OK, you can safely ignore it.
After you successfully install the Indigo nodes and restart Eclipse, you should be able to see the new nodes in the "Community Nodes/Indigo" section. Also, some example workflows are available in 099_Community/07_Indigo directory of the KNIME Example Flow Server.
Screenshots
R-Group Decomposition
Structure Validation
Fingerprint-Based Clustering
Feedback
You are welcome to post your bug-reports and suggestions about our KNIME nodes to the Indigo forum at the KNIME Tech. Topics related to the core Indigo library may, as always, be posted into our Google groups.