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0x_​Bonus_​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 0x_Bonus_R-Group-Decomposition with EnumerationThis 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 combos7 R-groupsMolecular 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 RDKit R-GroupDecomposition 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 0x_Bonus_R-Group-Decomposition with EnumerationThis 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 combos7 R-groupsMolecular 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 RDKit R-GroupDecomposition

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: 2024-01-14
Last update: 2024-11-23
Created with KNIME version: v4.6.0
Tags: RDKitR-Group Decomposition (RGD)ChemoinformaticsMaximum Common Substructure (MCS)SketcherLife SciencesEducation

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