Reaction Splitter

This node splits the input reactions into reactants, products and catalysts and writes result molecules into separate columns. Defines the output column type automatically.

Supported types:

  • Reaction: String, Rxn, Smiles, CML
  • Query reaction: String, Rxn, Smiles, SMARTS

The node is based on the Indigo cheminformatics toolkit.

Options

Target reaction column
Column name for the input reactions.
Extract reactants
Flag (append or skip) for molecule reactants column with specified name.
Extract products
Flag (append or skip) for molecule products column with specified name.
Extract catalysts
Flag (append or skip) for molecule catalysts column with specified name.
Input type
Treat input as: a reaction, a query reaction.
Treat X as pseudoatom
Treat the "X" atoms in Molfiles as pseudoatoms, not as "any halogen" query atoms.
Ignore stereochemistry errors
Ignore incorrectly specified stereochemistry on input structures, rather than sending the structures with stereochemistry errors to the "invalid molecules" table.
Treat query reaction as SMARTS
Treat string input for reaction as SMARTS.

Input Ports

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Table containing reactions or query reactions.

Output Ports

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The same as input, plus the columns with the created molecules.

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Installation

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

v5.9
Plugin provider: EPAM Systems, Inc.
Plugin version: 2.1.0.v202512081653
On NodePit since: 2025-12-11
Last update: 2026-01-07
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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