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geometry optimization

Works for alvaDesc 3D descriptors - Some molecules cannot be optimized - Also gives different values from above for alvaDesc 3D descriptors Had to do the worflow this way for molecules to be recognized byalvaDesc This crashes knime. smilesnot all are optimized!3D coords1 conformer per moleculerdkit mol tocdk molcdk mol tosdf molAlvaDescUFF Table Creator Molecule Type Cast Templated ConformerGeneration (RDKit) RDKit OptimizeGeometry RDKit Add Hs RDKit GenerateCoords RDKit From Molecule RDKit AddConformers Molecule to CDK CDK to Molecule Descriptor RDKit Add Hs RDKit OptimizeGeometry Works for alvaDesc 3D descriptors - Some molecules cannot be optimized - Also gives different values from above for alvaDesc 3D descriptors Had to do the worflow this way for molecules to be recognized byalvaDesc This crashes knime. smilesnot all are optimized!3D coords1 conformer per moleculerdkit mol tocdk molcdk mol tosdf molAlvaDescUFF Table Creator Molecule Type Cast Templated ConformerGeneration (RDKit) RDKit OptimizeGeometry RDKit Add Hs RDKit GenerateCoords RDKit From Molecule RDKit AddConformers Molecule to CDK CDK to Molecule Descriptor RDKit Add Hs 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: najdt0
Created at: 2020-04-22
On NodePit since: 2022-02-06
Last update: 2024-12-21
Created with KNIME version: v4.1.2

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