RDKit Functional Group Filter

This node can be used for filtering sets of molecules based on named substructures (functional groups based on SMARTS). Note that the default definitions are constructed to try and define functional groups relevant for reactivity; consequently groups like -CF3 do not match the halogen pattern.

Options

RDKit mol column
It specifies which column contains the set of RDKit molecules.
Functional group definition configuration
Lets the user define a customized functional group definition file. The default built-in definitions will be used when no file is specified.
  • Default: Loads the default configuration file.
  • Custom: Specify a configuration file.
Selected definition file
Specify a custom functional group definition file to use.
Enable recording in the following new column
If checked, an additional column (the name can be specified) containing the first non-matching pattern is added to the table of failing molecules.
Column name for first non-matching pattern
Name of the new column in the failed molecules table that will contain the first non-matching pattern.
Functional group filter conditions
Defines the conditions for filtering molecules. Select the ones that need to be applied on the molecules. If no filter pattern is selected, molecules will not be filtered at all. Each condition has a qualifier (e.g. "Less than or equal", "Equals") and a count for comparison.
  • Group condition: Whether this functional group condition is active and shall be applied during filtering.
  • Group name: The unique name of the functional group (populated from the definition file).
  • Qualifier: The comparison qualifier to apply when counting occurrences of this functional group.
  • Count: The number of occurrences to compare against using the qualifier.

Input Ports

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Table containing a set of RDKit molecules.
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The file system connection.

Output Ports

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Table containing molecules that pass the filter.
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Table containing molecules that do not pass the filter.

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Installation

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

v5.12
Plugin provider: Novartis
Plugin version: 6.0.0.v202607101001
On NodePit since: 2026-07-06
Last update: 2026-07-24
Tags: Modern UI
KNIME versions: v5.12, v5.11, v5.10, v5.9, v5.8, v5.7, v5.6, v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6

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