Highlighter

This node highlights the structure atoms and bond by indices privided in a column value. Indices can be separated by space or comma.

Supported types:

The node is based on the Indigo cheminformatics toolkit.

Options

Target Column: The column that contains molecule structures
Append Column: Appends a new structure column (with the name as specified in the text field) if checked, replaces the original column otherwise.
Clear Highlighting: Option to clear any previous highlighting.
Highlighted Atoms Indices: The column that contains indices of highlighted bonds.
Highlighted Bonds Indices: The column that contains indices of highlighted bonds.
Input type: Treat input as: a molecule
Treat X as pseudoatom: Treat the "X" atoms in Molfiles as pseudoatoms, not as "any halogen" query atoms
Ignore stereochemistry errors: Ignore incorrectly specified stereochemistry on input structures, rather than sending the structures with stereochemistry errors to the "invalid molecules" table.

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To use this node in KNIME, install the extension Indigo KNIME integration from the below update site following our NodePit Product and Node Installation Guide:

v5.9

Plugin provider: EPAM Systems, Inc.

Plugin version: 2.1.0.v202512081653

On NodePit since: 2025-12-11

Last update: 2026-01-06

KNIME versions: v5.9, v5.8, v5.7, v5.6, v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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