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PMI Plotting Example

PMI Plotting Example
Generate conformers and filter by RMSD between conformersTop route - using RDKit nodesLower route - using Vernalis node which offers most features of the top route in a more convenientpackage Calculate PMIs (npr1, npr2) Plot PMI Triangles* PMI Scatter Plot - the conventional plot type* PMI Kernel Density Plot - useful when you havelarge numbers of conformers* PMI Triangle Convex Hull plot - shows conformersfor indiviudal molecules in separate groups ('Hulls') Node 2Node 3Node 4Node 5Node 6Node 7Node 8Node 9Node 10Node 11Node 12Node 13Node 14Node 15Node 16 SDF Reader RDKit AddConformers RDKit Add Hs RDKit Remove Hs RDKit RMSD Filter Principal Moment of Intertia(PMI)-Derived Properties PMI TriangleScatter Plot PMI KernelDensity Plot PMI TriangleConvex Hull Plot RDKit Remove Hs Principal Moment of Intertia(PMI)-Derived Properties Templated ConformerGeneration (RDKit) Ungroup Principal Moment of Intertia(PMI)-Derived Properties PMI TriangleScatter Plot RDKit OptimizeGeometry Generate conformers and filter by RMSD between conformersTop route - using RDKit nodesLower route - using Vernalis node which offers most features of the top route in a more convenientpackage Calculate PMIs (npr1, npr2) Plot PMI Triangles* PMI Scatter Plot - the conventional plot type* PMI Kernel Density Plot - useful when you havelarge numbers of conformers* PMI Triangle Convex Hull plot - shows conformersfor indiviudal molecules in separate groups ('Hulls') Node 2Node 3Node 4Node 5Node 6Node 7Node 8Node 9Node 10Node 11Node 12Node 13Node 14Node 15Node 16SDF Reader RDKit AddConformers RDKit Add Hs RDKit Remove Hs RDKit RMSD Filter Principal Moment of Intertia(PMI)-Derived Properties PMI TriangleScatter Plot PMI KernelDensity Plot PMI TriangleConvex Hull Plot RDKit Remove Hs Principal Moment of Intertia(PMI)-Derived Properties Templated ConformerGeneration (RDKit) Ungroup Principal Moment of Intertia(PMI)-Derived Properties PMI TriangleScatter Plot RDKit OptimizeGeometry

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

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Created by: S.Roughley
Created at: 2022-10-18
On NodePit since: 2022-10-21
Last update: 2024-12-26
Created with KNIME version: v4.6.3
Tags: PMIPrincipal Moments of Inertianpr1npr2VernalisPlottingTriangle plotRodDiscSphere

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