RDKit 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.

The reaction can either be defined by a SMARTS pattern in the dialog or by providing a Rxn value at the third input port.

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.
Rxn column: The column from the third table containing the Rxn. Only used when a reaction table is connected to the third input port.
Reaction SMARTS: A reaction SMARTS describing the reaction. Only used when no reaction table is connected to the third input port. For a description of the format, please have a look in The RDKit Book.
Randomize reactants: If checked, random reactants will be picked for the reactions.
Maximum number of random reactions: Specify here the maximum number of reactions to be calculated. Note: When picking a number higher than a million and switching on Matrix expansion this can lead to memory issues.
Random seed: Specify here a seed for the random number generator or -1 to use it without a seed.
Uniquify products: Enable this option to filter out duplicates of products caused by symmetry in molecules. Only the first of multiple encountered products will show up in the result table.
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 are combined pairwise (row by row).
Include additional columns from reactant input tables into product output table: Enable this option in order to select additional data columns from reactant input tables to be included into the result table.
Additional columns from Reactant #1 table: Selection of additional data columns from reactant #1 input table.
Additional columns from Reactant #2 table: Selection of additional data columns from reactant #2 input table.

Input Ports

: Data with RDKit Mol column.
: Data with RDKit Mol column.
: Table with reaction values; if there are multiple rows only the first row is considered.

Output Ports

: Product molecules.

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Installation

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

v5.12

Plugin provider: Novartis

Plugin version: 6.0.0.v202607101001

On NodePit since: 2026-07-06

Last update: 2026-07-23

Tags: Modern UI

KNIME versions: v5.12, v5.11, v5.10, 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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