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Substructure Matcher

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

This node accepts a table with structures (supports reactions and molecules) and a table with query structures, and divides the first table into three sets: one with all rows that contain the specified query structures as a substructure, the other with all structures that do not contain it, the last one gathers all the rows with invalid data.

Supported types:

  • Molecule: String, SDF, Smiles, CML, Mol, InChI
  • Reaction: String, RXN, SMILES

The node is based on the Indigo cheminformatics toolkit.


Target column
The column that contains molecule or reaction structures.
Query structures column
The column that contains the query structure.
Substructure settings
Substructure settings that needs to be satisfied for all query structures or at least for a specified number of them.
Append queries row ID column
The column that contains all the meeting the conditions rows.
Append match count column
The column that contains the appropriate molecules amount.
Input type
Treat input as: a molecule, as a 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 input query string as SMARTS
Treat input string to create a query as SMARTS.

Input Ports

Table containing molecules or reactions.
Table containing the query structure.

Output Ports

Rows with matched structures.
Rows with unmatched structures.

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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