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PMI Plotting Example

A simple example workflow of how to use the various PMI (Principal Moments of Inertia) plotting nodes

Generate conformers and filter by RMSD between conformers Top route - using RDKit nodes Lower route - using Vernalis node which offers most features of the top route in a more convenient package
Calculate PMIs (npr1, npr2)
Plot PMI Triangles * PMI Scatter Plot - the conventional plot type * PMI Kernel Density Plot - useful when you have large numbers of conformers * PMI Triangle Convex Hull plot - shows conformers for indiviudal molecules in separate groups ('Hulls')
SDF Reader
RDKit Add Conformers
RDKit Add Hs
RDKit Remove Hs
RDKit RMSD Filter
Principal Moment of Intertia (PMI)-Derived Properties
PMI Triangle Scatter Plot
RDKit Remove Hs
PMI Kernel Density Plot
Ungroup
PMI Triangle Convex Hull Plot
Principal Moment of Intertia (PMI)-Derived Properties
Principal Moment of Intertia (PMI)-Derived Properties
Templated Conformer Generation (RDKit)
SDF Reader
RDKit Aromatizer
PMI Triangle Scatter Plot
RDKit Optimize Geometry

Nodes

Extensions

Links

Download

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

Download Workflow
Created by: S.Roughley
Created at: 2022-10-18
On NodePit since: 2025-12-25
Last update: 2025-12-25
Created with KNIME version: v5.8.0
Tags: PMIPrincipal Moments of Inertianpr1npr2VernalisPlottingTriangle plotRodDiscSphere

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