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02a_​R-Group_​Decomposition with Enumeration

02a_R-Group_Decomposition Bonus material

This workflow demonstrates how to perform R-Group Decomposition using the RDKit community extension and the enumeration of the library using the Python and the RDKit integrations.
The workflow has several steps
I. Compute MCS.
II. Perform R-Group Decomposition.
III. Find how many molecules with each combination of the two selected R-groups are in the dataset.
IV. Visualize the results of the R-group decomposition.

Bonus: Enumerate missing compounds using the python script and the RDKit nodes. Make sure to define the python environment in the File > Preferences. For more details on installation of rdkit inside your python/conda environment please see https://www.rdkit.org/docs/Install.html






Visualize the results of the R-group decomposition. III. Find how many molecules with each combination of thetwo selected R-groups are in the dataset. II. Perform R-Group Decomposition I. Compute MCS 02_R-Group-DecompositionThis is an example workflow to perform R-Group Decomposition. The workflow has several steps. See Description for more details. II. Perform R-Group Decomposition I. Draw the core Bonus Content: enumerating missing compounds Hiliting!get counts0.8core 7 R-groupsmoleculesr-groupsR-groupsinput.tableSplit out moleculeswe've already seenJust for the demoUniquify on SMILESCreate at most 100K possiblesidechain combosMolecular Sketcher Pivoting RDKit MCS RDKit From Molecule RDKit R-GroupDecomposition Component Embed images forthe R-groups (SVG) Render to images Pick R-groups forvisualization RDKit R-GroupDecomposition Table Reader Column Filter RDKit Canon SMILES Reference RowSplitter Enumerate molecules fromcore and sidechains Pick random subset Add core asworkflow variable DuplicateRow Filter Table Rowto Variable Python Script Visualize the results of the R-group decomposition. III. Find how many molecules with each combination of thetwo selected R-groups are in the dataset. II. Perform R-Group Decomposition I. Compute MCS 02_R-Group-DecompositionThis is an example workflow to perform R-Group Decomposition. The workflow has several steps. See Description for more details. II. Perform R-Group Decomposition I. Draw the core Bonus Content: enumerating missing compounds Hiliting!get counts0.8core 7 R-groupsmoleculesr-groupsR-groupsinput.tableSplit out moleculeswe've already seenJust for the demoUniquify on SMILESCreate at most 100K possiblesidechain combosMolecular Sketcher Pivoting RDKit MCS RDKit From Molecule RDKit R-GroupDecomposition Component Embed images forthe R-groups (SVG) Render to images Pick R-groups forvisualization RDKit R-GroupDecomposition Table Reader Column Filter RDKit Canon SMILES Reference RowSplitter Enumerate molecules fromcore and sidechains Pick random subset Add core asworkflow variable DuplicateRow Filter Table Rowto Variable Python Script

Nodes

Extensions

Links

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
Created by: daria_knime
Created at: 2020-04-16
On NodePit since: 2022-05-30
Last update: 2026-01-22
Created with KNIME version: v4.5.1
Tags: RDKitR-Group Decomposition (RGD)ChemoinformaticsMaximum Common Substructure (MCS)SketcherLife SciencesEducation

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