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

Input Molecules - RDKit Mol column (1st table): The column containing molecules.
Input Scaffolds - Core Input Column (2nd table): If second table is connected, the column containing cores as RDKit Molecules, SMARTS, SMILES or SDF.
Input Scaffolds - Strict Parsing of Mol Blocks: When SDF molecules are used as cores, this option sets the tolerance level for parsing mol blocks. The default value for new nodes is defined in RDKit Nodes / RDKit Types preferences. (Introduced in December 2022)
Input Scaffolds - Core SMARTS: If no second table is connected, one or multiple new-line separated SMARTS can be defined as the cores to be used.
Output Handling - Add matching SMARTS core: Flag to be set to add a column that contains the matching core from SMARTS input.
Output Handling - Core column name: The column name for the SMARTS core column, if it is set to be added.
Output Handling - 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 as substructure with the Rx attachments without query features.
Output Handling - Explicit core column name: The column name for the matching explicit core column, if it is set to be added.
Output Handling - Use atom maps: Flag to be set to control atom properties of the matching explicit core.
Output Handling - Use R-labels: Flag to be set to control atom properties of the matching explicit core.
Output Handling - Fail if no matching R-Groups are found: Flag to be set to detect Rx columns that are completely empty and remove them.
Output Handling - 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.

Advanced

Labels to recognize R-Groups in scaffolds: Enable or disable one or multiple labels to be used to recognize R-Groups in scaffolds. At least one item need to be picked.
Matching strategy: Select how matches shall be found.
Labeling for R-Groups output: Enable or disable options now to label R-Groups in the ouput.
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 consists 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 Tests Feature from the below update site following our NodePit Product and Node Installation Guide:

v5.3

A zipped version of the software site can be downloaded here.

Plugin provider: Novartis

Plugin version: 5.0.0.v202407311957

On NodePit since: 2024-09-28

Last update: 2024-11-21

KNIME versions: 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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