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Substructure Match Counter

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

This node counts the number of unique independent matches of a given query file in each molecule of the input table

Supported types:

  • Molecule: String, SDF, Smiles, CML, Mol, InChI

The node is based on the Indigo cheminformatics toolkit.


Target molecule column
The column that contains molecule structures.
Query molecule column
The column that contains the query molecule.
New column name
Name of the new column with the counter(s) to append.
  • By atoms: "CCC" matches "C1CC1" once
  • By bonds: "CCC" matches "C1CC1" three times
  • None: "CCC" matches "C1CC1" six times
Highlight all matches
Highlight matches in the input structure (available only in "uniqueness by atoms" mode).
Append column
Append a new column with highlighted structures (of not set, the original column is modified).
Input type
Treat input as: a molecule.
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.
Table containing the query molecule.

Output Ports

The same as input molecules, plus an extra column with match counters.

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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