Dearomatizer

This node converts one of the incoming columns with chemical structures into the Kekule form. The new column is appended to the input table or replaces an old target column.

Supported types:

Molecule: String, SDF, Smiles, CML, Mol, InChI
Reaction: String, RXN, SMILES

The node is based on the Indigo cheminformatics toolkit.

Options

Target Column: The column that contains molecule or reaction structures.
Append Column: Appends a new structure column (with the name as specified in the text field) if checked, replaces the original column otherwise.
Input type: Treat input as: a molecule, a reaction.
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

: Table containing molecule or reaction structures.

Output Ports

: The same as input, with dearomatized structures

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Installation

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:

v5.3

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

Plugin provider: EPAM Systems, Inc.

Plugin version: 2.1.0.v202406240930

On NodePit since: 2024-07-11

Last update: 2024-11-22

KNIME versions: 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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