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Explore Molecular Properties

This workflow snippet shows a possible way to prepare and visually explore a dataset with molecules.
We configure the File Reader node to read the SMILES strings of the input data as smiles format. Next we calculate the basic physico chemical properties using the RDKit Descriptor Calculation node. Then we generate the images of the molecules using the Renderer to Image node. Finally, we combine the Parallel Coordinates Plot and the Tile View nodes in the component "Explore Properties". By combining these two nodes that operate on the same data table in one component, we automatically achieve the interactivity of the combined view. To open the view, simply right-click on the component "Explore Data" and select "Interactive View: Explore Properties" in the dropdown.

Requirements:
KNIME Base Chemistry Types & Nodes
RDKit KNIME Intergration


Explore Molecular PropertiesThis workflow snippet shows a way to prepare and visually explore the physico-chemical properties of molecules. For more information please check the worklfow description on the right side. If it's not shown by default, set it here: View -> Description.Required KNIME extensions:KNIME Base Chemistry Types & NodesRDKit KNIME Intergration Read input moleculesWe configure the File Reader torecognize the SMILES format. To do that, open theconfiguration dialog of thenode; click on the column withthe SMILES in the data preview.This will open a pop-up windowwhere you can select SMILESin the "Type" field. Compute descriptorsWe add the physico-chemicalproperties we want to calculateto the right box (in the greenframe) by selecting the propertyand clicking on "Add >>" buttonin the cofiguration dialog.Alternatively, you can justdouble-click on the property. Create images for themoleculesWe generate png images of themolecules using the RDKit 2Ddepiction Renderer andappend a column "Mol_image"to the result table. Explore propertiesTo view the content ofcomponent, Ctrl/Cmd + doubleclick on it. To see the Interactive View,execute the component andthen right click -> InteractiveView: Explore PropertiesIn the Interactive View: 1. Selecta few lines and the images ofthe molecules will appearbelow the plot; 2. Rearrangethe vertical axes by drag&dropto find possible hiddenrelationships in the data. phys chem propertiessampleinput datacreate images RDKit DescriptorCalculation File Reader Explore Properties Renderer to Image Explore Molecular PropertiesThis workflow snippet shows a way to prepare and visually explore the physico-chemical properties of molecules. For more information please check the worklfow description on the right side. If it's not shown by default, set it here: View -> Description.Required KNIME extensions:KNIME Base Chemistry Types & NodesRDKit KNIME Intergration Read input moleculesWe configure the File Reader torecognize the SMILES format. To do that, open theconfiguration dialog of thenode; click on the column withthe SMILES in the data preview.This will open a pop-up windowwhere you can select SMILESin the "Type" field. Compute descriptorsWe add the physico-chemicalproperties we want to calculateto the right box (in the greenframe) by selecting the propertyand clicking on "Add >>" buttonin the cofiguration dialog.Alternatively, you can justdouble-click on the property. Create images for themoleculesWe generate png images of themolecules using the RDKit 2Ddepiction Renderer andappend a column "Mol_image"to the result table. Explore propertiesTo view the content ofcomponent, Ctrl/Cmd + doubleclick on it. To see the Interactive View,execute the component andthen right click -> InteractiveView: Explore PropertiesIn the Interactive View: 1. Selecta few lines and the images ofthe molecules will appearbelow the plot; 2. Rearrangethe vertical axes by drag&dropto find possible hiddenrelationships in the data. phys chem propertiessampleinput datacreate images RDKit DescriptorCalculation File Reader Explore Properties Renderer to Image

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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: daria_knime
Created at: 2021-02-07
On NodePit since: 2021-12-18
Last update: 2024-04-30
Created with KNIME version: v4.3.2
Tags: CheminformaticsMoleculeData VisualizationLife Sciences

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