04_​Databased_​MMP_​Example

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This is a more complex Matched Molecular Pairs (MMP) example, in which we demonstrate storing fragmentations and transforms in a database, and adding new fragmentations and pairs from new molecules, as might be performed with routine updates to a registration or compound database.
The datasets are based on the same data as the 'Simple MMP Example'. The first represents an existing compound set, and the second a set of new compounds (seeded with a few duplicates).
We use the multi-cut version of the node to perform 1-10 cuts on the 'existing' set first and we generate pair transforms. Fragments, transforms and failed rows are all databased for later recall (here we use an sqlite db in the same folder that contains the workflow - run this locally to create the DB file - it is quite big!)

The Vernalis fingerprint nodes are used to regenerate fingerprint columns from the databased representations

Nodes

• DB Writer6 ×
• Concatenate3 ×
• Column Filter2 ×
• Column Rename2 ×
• Column Rename (Regex)2 ×
• Show all 27 nodes

Extensions

• FeatureKNIME Base Chemistry Types & Nodes
• FeatureKNIME Base nodes
• FeatureKNIME Database
• FeatureSchrödinger Extensions for KNIME
• FeatureVernalis KNIME Nodes

Links

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