Canonical SMILES

This node takes a table containing a column with molecules or reactions as a target and append new column with these objects in canonical SMILES format (string representation).

Supported types:

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

The node is based on the Indigo cheminformatics toolkit.

Options

Target column: The column that contains molecules or reactions.
Append column: Name for the new column that contains the molecules/reactions in canonical SMILES format.
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 molecules or reactions.

Output Ports

: The same as input, but with a new string column containing canonical SMILES representations.

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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: 2026-01-10

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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