03_RDKit
This directory contains 8 workflows.
01_Clustering
This flow loads in some public data, generates fingerprints, and then does hierarchical clustering. Requirements: - RDKit Community nodes
02_Reaction_Enumeration
Demonstrates standard reaction-based library enumeration. The dataset used in this example workflow was taken from ZINC […]
03_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 […]
04_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 […]
05_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 […]
06_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 […]
07_RDKit_with_Java_Snippet_Example
Demonstrates using RDKit functionality directly inside the Java Snippet node. Requires KNIME 3.3+.
08_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