RDKit R-Group Decomposition

Performs an R-Group decomposition for an input RDKit mol column. The algorithm in RDKit was developed in 2018/2019. It is still in beta state and should be used with care. Results may vary in later versions.

Options

RDKit mol column: The column containing molecules.
Core input column (2nd table): If a second table is connected, the column containing cores as RDKit Molecules, SMARTS, SMILES or SDF. When no second table is connected, use the Core SMARTS text field below instead.
Strict parsing of mol blocks: When SDF molecules are used as cores, this option sets the tolerance level for parsing mol blocks. Only applicable when SDF-compatible columns are used as core input. The default value is defined in the RDKit preferences.
Core SMARTS: If no second table is connected, one or multiple new-line separated SMARTS can be defined as the cores to be used.
Add matching SMARTS core: Flag to be set to add a column that contains the matching core from SMARTS input.
Core column name: The column name for the SMARTS core column, if it is set to be added.
Add matching explicit core: Flag to be set to add a column that contains the matching explicit core based on the matching SMARTS and input molecule. It shows the real matching core derived from the input molecule.
Explicit core column name: The column name for the matching explicit core column, if it is set to be added.
Use atom maps: Flag to be set to control atom properties of the matching explicit core.
Use R-labels: Flag to be set to control atom properties of the matching explicit core.
Remove empty Rx columns: Flag to be set to detect Rx columns that are completely empty and remove them.
Fail if no cores are matching at all: Flag to be set to let the node fail if no matches for the provided cores have been found at all.
Labels to recognize R-Groups in scaffolds: Enable one or multiple labels to be used to recognize R-Groups in scaffolds. At least one item needs to be picked.
Matching strategy: Select how matches shall be found.
Labeling for R-Groups output: Enable options how to label R-Groups in the output.
Core alignment: Select how cores shall be aligned.
Match only at R-Groups: Flag to be set to find matches only at R-Groups.
Remove hydrogen only R-Groups: Flag to be set to remove R-Groups that consist only of hydrogens from matching.
Remove hydrogens post match: Flag to be set to remove all hydrogens in the resulting R-Groups output.

Input Ports

: Molecules as RDKit molecule, SMILES or SDF column.
: Cores as RDKit molecule, SMARTS, SMILES or SDF column.

Output Ports

: Table with matching core and decomposed R-Groups.
: Table with unmatched input rows.

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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, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7

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