Tuesday, February 18, 2014

RDKit Knime Workflows I

Things have been quiet lately since I spent a fair amount of time getting ready for last week's Knime UGM in Zürich. On Friday I did a 90 minute workshop that introduced some (I think) interesting and useful functionality that is available via the RDKit Knime nodes.

Over the next few days I will post slightly cleaned up versions of those workflows here.

Here's the first example, a workflow that uses some computed property filters and the PAINS substructure patterns to clean up a set of compounds:

In addition to the always useful descriptor calculator and substructure counter nodes, this also uses the RDKit Interactive Table, which has the nice feature of being able to display molecule renderings in column headers:

Until I figure out how to host these in a sensible way on a public knime server, I'll just provide things via dropbox links.
Here's the data directory that is used in this and all other workflows: https://db.tt/qSdJn0St
And here's the link to this workflow: https://db.tt/crzUy5i1

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