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03_​Template_​Enumeration

Template based enumeration

This workflow shows template-based enumeration (attaching side chains to a core). This flow also uses the constrained coordinate generation to make sure that when coordinates are generated the core is always oriented the same way.

The dataset used in this example workflow was taken from ZINC (http://zinc.docking.org/).

Requirements:
- RDKit Community Nodes

Demonstrates reading in a set of building blocks, flitering them, and thenusing a reaction to attach them to a template.Extensions required:RDKit Align molecules to templateConvert to SDFKeep 100Keep 100Carboxylic acids = 1Primary amines = 1Secondary amines = 0Read SMILESProcess SMILESEnumeratethe matrixNode 32 RDKit GenerateCoords RDKit To Molecule Row Sampling Row Sampling RDKit FunctionalGroup Filter RDKit FunctionalGroup Filter File Reader(deprecated) RDKit From Molecule RDKit Two ComponentReaction Smiles Reader Demonstrates reading in a set of building blocks, flitering them, and thenusing a reaction to attach them to a template.Extensions required:RDKit Align molecules to templateConvert to SDFKeep 100Keep 100Carboxylic acids = 1Primary amines = 1Secondary amines = 0Read SMILESProcess SMILESEnumeratethe matrixNode 32 RDKit GenerateCoords RDKit To Molecule Row Sampling Row Sampling RDKit FunctionalGroup Filter RDKit FunctionalGroup Filter File Reader(deprecated) RDKit From Molecule RDKit Two ComponentReaction Smiles Reader

Nodes

Extensions

Links

Download

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

Download Workflow
On NodePit since: 2022-09-28
Last update: 2024-12-17
Created with KNIME version: v4.6.2

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