03_​RDKit

This directory contains 8 workflows.

Icon01_​Clustering 

This flow loads in some public data, generates fingerprints, and then does hierarchical clustering. Requirements: - RDKit Community nodes

Icon02_​Reaction_​Enumeration 

Demonstrates standard reaction-based library enumeration. The dataset used in this example workflow was taken from ZINC […]

Icon03_​Template_​Enumeration 

This workflow shows template-based enumeration (attaching side chains to a core). This flow also uses the constrained coordinate generation to make sure […]

Icon04_​Chemical_​Transformations 

This workflow demonstrates use of the chemical transformation node, which applies a reaction repeatedly to a set of inputs. The dataset used in this […]

Icon05_​Working_​In_​3D 

This workflow demonstrates use of some of the RDKit's 3D functionality, including 2D->3D conversion and geometry optimization. The dataset used in this […]

Icon06_​Find_​Scaffolds_​And_​Sidechains 

Demonstrates use of RDKit functionality to identify the likely scaffold for a set of compounds from a paper and then determine the sidechains from the […]

Icon07_​RDKit_​with_​Java_​Snippet_​Example 

Demonstrates using RDKit functionality directly inside the Java Snippet node. Requires KNIME 3.3+.

Icon08_​Chemical_​Topic_​Modeling 

Demonstrates using KNIME text mining nodes to do chemical topic modeling following the approach described in https://dx.doi.org/10.1021/acs.jcim.7b00249