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Reaction Splitter

Indigo extensions for KNIME Workbench version 2.0.0.qualifier by EPAM Systems, Inc.

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.


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

Table containing reactions or query reactions.

Output Ports

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

Best Friends (Incoming)

Best Friends (Outgoing)



To use this node in KNIME, install Indigo KNIME integration from the following update site:


A zipped version of the software site can be downloaded here.

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