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_​01_​ChemicalLibraryEnumeration

Chemical Library Enumeration

Chemical Library Enumeration

This example flow will take an SDFile containing organic amines and acids and will perform a amide formation reaction. You can define the number of reactants that should be used to create the library. For the enumerated products the “Pfizer rules of 5” will be calculated and the products that violate the rule will be filtered out.
Finally a report is generated that shows a summary with 8 structures representing the library, a plot that shows the molecular weight distribution in the library and the products with the calculated parameters with a star plot based on these.
The resulting products can be downloaded as an SDFile.
The flow requires the RDKit and Indigo community nodes to be installed as well as CDK and R.
The flow is based on an example from Greg Landrum.

Summary Plot to reportGrid View to reportFormat for ReportMain table to reportSummary plot setupMain table setupGrid View SetupNode 273Row FiltersDownload ResultsNode 276Node 277Prompt for SDFileImage to Report Data to Report RDKit From Molecule Data to Report SDF Reader Metanode Main table setup Metanode Indigo nodes Metanode CDK properties RDKit Reaction File Upload Summary Plot to reportGrid View to reportFormat for ReportMain table to reportSummary plot setupMain table setupGrid View SetupNode 273Row FiltersDownload ResultsNode 276Node 277Prompt for SDFileImage to Report Data to Report RDKit From Molecule Data to Report SDF Reader Metanode Main table setup Metanode Indigo nodes Metanode CDK properties RDKit Reaction File Upload

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Extensions

Links

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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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On NodePit since: 2019-07-12
Last update: 2026-03-27
Created with KNIME version: v4.2.2

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