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Reaction Builder

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

This node combines the input molecules and creates reactions from given reactants, products and catalysts columns. Defines the output column type automatically.

Supported types:

  • Molecule: String, SDF, Smiles, CML, Mol, InChI
  • Query molecule: String, Smiles, Mol, SMARTS, SDF

The node is based on the Indigo cheminformatics toolkit.


Add reactants
Flag (append or skip) and column selection for molecule reactants.
Add products
Flag (append or skip) and column selection for molecule products.
Add catalysts
Flag (append or skip) and column selection for molecule catalysts.
Result reaction column name
Column name for the output molecules
Input type
Treat input as a reaction or as a query reaction
Output type
Result column type.
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 input String as SMARTS
Treat string input for molecule as SMARTS

Input Ports

Table containing molecules or query molecules

Output Ports

The same as input, plus the column with the created reactions
The same as input, contains invalid data (unconvertible to Indigo)

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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