CDK to Molecule

Converts the CDK molecules in one of the input table's columns into various string representations (SDF, Mol2, Smiles, CML).

This node uses CDK classes to parse and display structures.

Options

CDK Column: The column that contains the CDK molecules.
Replace Column: Select this to replace the CDK column with the column containing the converted string representations. Otherwise a new column will be appended.
New column name: Enter the name of the new column here if the original column is not replaced (see option above).
Destination format: Select the destination format here.

This node has no views

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.

To use this node in KNIME, install the extension KNIME-CDK from the below update site following our NodePit Product and Node Installation Guide:

v5.9

Plugin provider: KNIME GmbH, Konstanz and EMBL-EBI, Cambridge

Plugin version: 1.5.700.v202511141653

On NodePit since: 2025-12-11

Last update: 2026-01-10

KNIME versions: v5.9, v5.8, v5.7, v5.6, v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.