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.

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Workflows

• 01_R-Group_DecompositionKNIME Hub
• 01_R-Group_DecompositionKNIME Hub
• 01_R-Group_Decomposition_embed_imagesKNIME Hub
• 01_R-Group_Decomposition_embed_imagesKNIME Hub
• 02_R_Group_Decomposition_solutionKNIME Hub
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