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Combinatorial Reaction Enumeration (beta)

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

This node generates reactions by the specified reaction pattern and the input molecules. See the examples for more details.

Supported types:

  • Query reaction: String, Rxn, Smiles, SMARTS

The node is based on the Indigo cheminformatics toolkit.


Target reaction column
Column name for the input reactions.
Reactants 1 column
Column name for the input molecules.
Reactants 2 column
Column name for the input molecules.
New column name
Column name for the output reactions column.
Products count limit
Max value for products count.
Reaction type
Treat input as: a query reaction.
Molecule type
Treat input as a molecule.
Output column type
Output reactions column type (Rxn, Smiles)
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 with a single query reaction.
First molecules set
Optional second molecules set

Output Ports

Reactions generated by the specified reaction pattern and the input 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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