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Dearomatizer

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

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

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Table containing molecule or reaction structures.

Output Ports

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The same as input, with dearomatized structures

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

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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