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Highlighter

Indigo extensions for KNIME Workbench version 2.0.0.qualifier by EPAM Systems, Inc.

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:

  • Molecule: String, SDF, Smiles, CML, Mol, InChI

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.

Input Ports

Icon
Table containing a column with molecules

Output Ports

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The same as input, but with atoms and bonds highlighted

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install Indigo KNIME integration from the following update site:

KNIME 4.2

A zipped version of the software site can be downloaded here.

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Developers

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