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02 CCDC CSD Substructure Search

CCDC CSD Substructure Search

CCDC CSD Substructure Search

This example workflow illustrates the use of the CSD Substructure Search component. Queries may come from various sources, but must be in MOL format. The query substructure is highlighted in the output diagram, and a list of the labels of the atoms matched is also returned.

This example shows that suitable MOL-format queriesmay also be generated from SMILES input. Here we useRDKit Nodes to perform the conversion (double-click theMetaNode to see the details). Here we use (4-anilino) quinazoline as a substructure query.When using the Marvin Sketch node, the ' Structure type' option on thethe 'Output options' tab must be set to 'MolCell' or the CSDSubstructure Search component will not work correctly.Note that to change this option from the default of 'MrvCell', the'Change structure output' box must be checked first. CCDC CSD Substructure SearchThis example workflow illustrates the use of the CCDC CSD Substructure Search component. Queries may come from various sources, but must be in MOL format. The querysubstructure is highlighted in the output diagram, and a list of the labels of the atoms matched is also returned.The notes on visualisation of hits and on search filters in the CCDC CSD Text-Numeric Searches example workflow apply to other search types, so they are not discussed again here.Example files to be used in these workflows are included in this archive: http://downloads.ccdc.cam.ac.uk/KNIME/Example_Workflows.zipDownload and extract the archive, then replace /path/to in any configuration file paths with the full path to the folder into which you extracted the archive. The ' Load MOL files' utility is used to load multiplesubstructure queries from a folder of MOL-format files.Double-click the component to configure it to point to thecorrect folder on your system.These structres were drawn in in Marvin Sketch andexported as MOL-format molfiles. Inspection will show thatthe hit-list is the same as in the SMILES example above. The data table may be exported to a CSV file.As multi-line strings are problematic in some contexts, theMOL2 column and diagram are removed before export. Remove molfileView hitsQueries as SMILESDouble-click to accessthe individual filters.Export to fileRemovemulti-line columns CCDC Run Mercury Column Filter SMILES to MOL Table View MarvinSketch Table Creator CSD Search Filters CSV Writer Column Filter CCDC Load MOL files CCDC CSDSubstructure Search CCDC CSDSubstructure Search CCDC CSDSubstructure Search This example shows that suitable MOL-format queriesmay also be generated from SMILES input. Here we useRDKit Nodes to perform the conversion (double-click theMetaNode to see the details). Here we use (4-anilino) quinazoline as a substructure query.When using the Marvin Sketch node, the ' Structure type' option on thethe 'Output options' tab must be set to 'MolCell' or the CSDSubstructure Search component will not work correctly.Note that to change this option from the default of 'MrvCell', the'Change structure output' box must be checked first. CCDC CSD Substructure SearchThis example workflow illustrates the use of the CCDC CSD Substructure Search component. Queries may come from various sources, but must be in MOL format. The querysubstructure is highlighted in the output diagram, and a list of the labels of the atoms matched is also returned.The notes on visualisation of hits and on search filters in the CCDC CSD Text-Numeric Searches example workflow apply to other search types, so they are not discussed again here.Example files to be used in these workflows are included in this archive: http://downloads.ccdc.cam.ac.uk/KNIME/Example_Workflows.zipDownload and extract the archive, then replace /path/to in any configuration file paths with the full path to the folder into which you extracted the archive. The ' Load MOL files' utility is used to load multiplesubstructure queries from a folder of MOL-format files.Double-click the component to configure it to point to thecorrect folder on your system.These structres were drawn in in Marvin Sketch andexported as MOL-format molfiles. Inspection will show thatthe hit-list is the same as in the SMILES example above. The data table may be exported to a CSV file.As multi-line strings are problematic in some contexts, theMOL2 column and diagram are removed before export. Remove molfileView hitsQueries as SMILESDouble-click to accessthe individual filters.Export to fileRemovemulti-line columns CCDC Run Mercury Column Filter SMILES to MOL Table View MarvinSketch Table Creator CSD Search Filters CSV Writer Column Filter CCDC Load MOL files CCDC CSDSubstructure Search CCDC CSDSubstructure Search CCDC CSDSubstructure Search

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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: flatk
Created at: 2020-07-08
On NodePit since: 2020-09-10
Last update: 2024-11-21
Created with KNIME version: v4.1.3

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