RDKit Two Component Reaction

This Node Is Deprecated — This version of the node has been replaced with a new and improved version. The old version is kept for backwards-compatibility, but for all new workflows we suggest to use the version linked below.
Go to Suggested ReplacementRDKit Two Component Reaction
Applies a reaction to two RDKit Mol columns.

The output table contains a row for each product produced by applying the reaction to the inputs.
Each row contains the product molecule, index information, and the reactant molecules that were used.

Options

Reactants 1 RDKit Mol column
The column containing the first reactant molecules
Reactants 2 RDKit Mol column
The column containing the second reactant molecules
Reaction SMARTS
A reaction SMARTS describing the reaction.
For a description of the format, please have a look in The RDKit Book.
Use Reaction from RXN file
If you want to use a reaction file rather than a smarts pattern, select this box and choose the RXN file in the file browser.
Do Matrix Expansion
If checked, each reactant 1 will be combined with each reactant 2 yielding the combinatorial expansion of the reactants. If not checked, reactants 1 and 2 will be combined sequentially, with the longer list determining the number of output rows.

Input Ports

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Data with RDKit Mol column
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Data with RDKit Mol column

Output Ports

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Product molecules

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Installation

To use this node in KNIME, install the extension RDKit Nodes Tests Feature from the below update site following our NodePit Product and Node Installation Guide:

v5.9
Plugin provider: Novartis
Plugin version: 5.2.1.v202507231837
On NodePit since: 2025-12-12
Last update: 2026-01-11
Tags: Deprecated
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

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