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Highlighting Fingerprint Bits

Displaying information about fingerprint bits.

This workflow demonstrates how to use RDKit functionality to highlight the atoms and bonds involved in a particular fingerprint bit.

Displaying information about fingerprint bits.This workflow demonstrates how to use RDKit functionality tohighlight the atoms and bonds involved in a particular fingerprintbit. Extensions required:RDKit KNIME extensionsPython scripting (correctly configured, with an RDKit installaccessible from Python) This piece is mainly here for the demo. It loops over the setof molecules provided as input, generates fingerprints forthem (make sure the fingerprint parameters here matchthe ones in the "Highlight Morgan Bit" metanode below),and then picks the 10 most frequently occuring bits. Read in a set of SMILES and convert them into RDKit molecules.This demo uses a set of ChEMBL molecules where CYP measurements have beendone Highlight the atom environments from the fingerprints.The central atom is highlighted in blue, the bonds in red.The loop expects the input table to contain the bits ofinterest. Last step: combine thehighlight columns with theinput data: Node 1Node 2Node 4Node 5Node 14Node 23Node 24Node 26Node 27Node 28 Table Reader Column Filter Molecule Type Cast Row Filter RDKit From Molecule Table Row ToVariable Loop Start HighlightMorgan Bit Loop End (ColumnAppend) Joiner Identifyinteresting bits Displaying information about fingerprint bits.This workflow demonstrates how to use RDKit functionality tohighlight the atoms and bonds involved in a particular fingerprintbit. Extensions required:RDKit KNIME extensionsPython scripting (correctly configured, with an RDKit installaccessible from Python) This piece is mainly here for the demo. It loops over the setof molecules provided as input, generates fingerprints forthem (make sure the fingerprint parameters here matchthe ones in the "Highlight Morgan Bit" metanode below),and then picks the 10 most frequently occuring bits. Read in a set of SMILES and convert them into RDKit molecules.This demo uses a set of ChEMBL molecules where CYP measurements have beendone Highlight the atom environments from the fingerprints.The central atom is highlighted in blue, the bonds in red.The loop expects the input table to contain the bits ofinterest. Last step: combine thehighlight columns with theinput data: Node 1Node 2Node 4Node 5Node 14Node 23Node 24Node 26Node 27Node 28 Table Reader Column Filter Molecule Type Cast Row Filter RDKit From Molecule Table Row ToVariable Loop Start HighlightMorgan Bit Loop End (ColumnAppend) Joiner Identifyinteresting bits

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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: glandrum
Created at: 2016-02-22
On NodePit since: 2019-10-03
Last update: 2024-11-21
Created with KNIME version: v4.0.0
Tags: RDKit fingerprints visualization

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