Substructure Match Counter

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.

Options

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.
Uniqueness
  • 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

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Table containing molecules.
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Table containing the query molecule.

Output Ports

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

Popular Predecessors

Popular Successors

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Links

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Installation

To use this node in KNIME, install the extension Indigo KNIME integration from the below update site following our NodePit Product and Node Installation Guide:

v5.9
Plugin provider: EPAM Systems, Inc.
Plugin version: 2.1.0.v202512081653
On NodePit since: 2025-12-11
Last update: 2026-01-10
KNIME versions: v5.9, v5.8, v5.7, v5.6, v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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