Standardizer

This node accepts a table with molecules and returns table with standardized molecules in accordance to applied options. In case of activation multiple options the order of applied modifications corresponds to the order of options in the list of picked options.

Supported types:

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

The node is based on the Indigo cheminformatics toolkit.

Options

Target Column
The column that contains molecule or query 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.
Input type
Treat input as: a molecule, a query 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.
Options
Two listboxes: the left one contains all the possible standardizing options to apply (can be filtered); the right one contains all options which are going to be applied (Note: options order matters). Also there is a control box allowing to move options between the listboxes. Corresponding mouse over tooltip containing option' description is available for every option.

Input Ports

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Table containing molecule or query molecule structures.

Output Ports

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The same as input, with standardized molecules.

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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:

v5.9
Plugin provider: EPAM Systems, Inc.
Plugin version: 2.1.0.v202512081653
On NodePit since: 2025-12-11
Last update: 2026-01-23
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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