One of the cool new features of KNIME Analytics Platform 3.3 is the ability to use the Java Snippet node with objects and functions that are defined in KNIME extensions. This allows an interesting and powerful new way to work with extensions that are compatible with the new functionality (more on the small amount of work required for that in a separate post, but for those who want to get a head start, here’s a link to the commit that added the functionality to the RDKit nodes). This post will demonstrate how to use the RDKit Java wrappers from within a KNIME Java Snippet node. Though this blog post uses cheminformatics functionality from the RDKit as a demonstration, the new feature can also be used to work with things like images, XML and JSON documents, and SVGs.
We’ll be working with the Java Snippet node, here’s some more information about that. Needless to say, you need to have KNIME 3.3 (or later) with the RDKit community nodes installed. As of this writing you need the nightly build of the RDKit nodes; the update site (http://update.knime.org/community-contributions/trunk) is linked from the KNIME Community site.
Example 1: Working with RDKit Molecules.
Let’s start by reading in a set of SMILES from a file, converting those to RDKit molecules, and then adding a Java Snippet node. Here’s the fragment of the workflow:
