SMARTS Query

Matches a list of molecules against a list of SMARTS patterns. Molecules that match at least one SMARTS pattern are included in the first output table. Molecules that match no SMARTS pattern are directed to the second output table. Stereochemistry is supported by default. If "Match Unique" is selected, a list column with the unique count of matches is appended. The query order is preserved.

Options

Column with molecules: Select the column that contains the molecules.
Column with SMARTS: Select the column that contains the SMARTS strings (SMARTSCell type).
Count unique: Appends a list column with unique matches.
Record match positions: Appends the matched atoms and bonds. Does not differentiate between the matches.

Input Ports

: Table that contains at least one column with CDK molecules.
: Table that contains at least one column with SMARTS queries.

Output Ports

: Table with molecules that match at least one query.
: Table with molecules that do not match any of the queries.

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Installation

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

v5.9

Plugin provider: KNIME GmbH, Konstanz and EMBL-EBI, Cambridge

Plugin version: 1.5.700.v202511141653

On NodePit since: 2025-12-11

Last update: 2026-01-19

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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