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Sanitizing query SMARTS

How to sanitize SMARTS

In the last snippet we have shown how to align molecules according to drawn SMARTS. This works fine just like this in some cases, but especially for structures involving aromaticity it fails. In this workflow snippet we will show how to generate sanitized query SMARTS using two RDKit nodes. We configure the sanitization of the "drawn" SMARTS in the advanced tab of the RDKit from Molecule node. To compare the sanitized and the unsanitized SMARTS, check the output of the RDKit to Molecule node. Right-click on the column headers, and change the renderer to String.Rrecognize how the sanitized SMARTS allows double-bonds at any position.

Required extension: RDKit







This workflow snippet demonstrates how to sanitize SMARTS from a drawn structure, so they can be used as query or to align molecules. For moreinformation, please read the workflow description. Sanitize the drawn structure Create a flow variable containing the SMARTSDraw the scaffold to which the molecules should be aligned toConvert it to SMARTSSet the flow variable with the SMARTS as template, and all input molecules get depicted with the benzoic acid in the same orientationInput moleculescontaining benzoic acidRDKit From Molecule Table Rowto Variable Molecular Sketcher RDKit To Molecule RDKit GenerateCoords File Reader(Complex Format) This workflow snippet demonstrates how to sanitize SMARTS from a drawn structure, so they can be used as query or to align molecules. For moreinformation, please read the workflow description. Sanitize the drawn structureCreate a flow variable containing the SMARTSDraw the scaffold to which the molecules should be aligned toConvert it to SMARTSSet the flow variable with the SMARTS as template, and all input molecules get depicted with the benzoic acid in the same orientationInput moleculescontaining benzoic acidRDKit From Molecule Table Rowto Variable Molecular Sketcher RDKit To Molecule RDKit GenerateCoords File Reader(Complex Format)

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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: 2024-11-21
Created with KNIME version: v4.4.0
Tags: Life SciencesSanitizationSMARTSCheminformatics

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