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Align the orientation of molecules

Aligning molecule orientation

This workflow demonstrates how to align molecules according to a substructure, so they are all shown in the same orientation (in this example accoring to the carbocylic acid). The bit of the molecules according to which they should be aligned is drawn in the sketcher component. The resulting SMARTS is used in the RDKit Generate Coords node to change the 2D coordinates of the atoms (set the rendering to SDF by right-clicking on the column header and check the changed coordinates).

Required extension: RDKit






This workflow snippet demonstrates how to align molecules so they all have the same orientation, in this example with the carboxylic group to theright. For more information, please read the workflow description. Draw the scaffold, in this case the carboxylic acid. Export it as SMARTSSet the flow variable with the SMARTS as template, and all input molecules get depicted with the carboxylic group in the same orientationCreate a flow variable containing the SMARTSInput moleculeswith carboxylic groups Molecular Sketcher RDKit GenerateCoords Table Rowto Variable File Reader Molecule Type Cast This workflow snippet demonstrates how to align molecules so they all have the same orientation, in this example with the carboxylic group to theright. For more information, please read the workflow description. Draw the scaffold, in this case the carboxylic acid. Export it as SMARTSSet the flow variable with the SMARTS as template, and all input molecules get depicted with the carboxylic group in the same orientationCreate a flow variable containing the SMARTSInput moleculeswith carboxylic groupsMolecular Sketcher RDKit GenerateCoords Table Rowto Variable File Reader Molecule Type Cast

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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: glandrum
Created at: 2020-05-19
On NodePit since: 2021-12-18
Last update: 2024-04-27
Created with KNIME version: v4.4.0
Tags: Life SciencesMoleculesOrientationCheminformatics

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