Molecule Properties

Create new columns holding molecular properties, computed for each structure. The computations are based on the Indigo toolkit and include number of heavy atoms, molecular weight, number of aromatic atoms, and others.

Supported types:

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

The node is based on the Indigo cheminformatics toolkit.

Options

Target Column: Column containing the molecular structures.
Properties: Move the available properties into the INCLUDE (right) list.
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

: Table containing molecule structures.

Output Ports

: As input but with additional columns (one for each calculated property).
: Rows with invalid data: data cannot be translated into Indigo object.

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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: 2026-01-06

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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