Component Separator

This node decomposes the input molecules into connected components and writes the components into the output table columns. The biggest component goes into the first column, the second biggest component goes into the second column, and so on.

Supported types:

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

The node is based on the Indigo cheminformatics toolkit.

Options

Target column: The column that contains molecule structures.
New column prefix: Each of the new columns will be named with this prefix + number (1,2,3,..)
Limit component number: Flag for skipping molecule components. The node writes first components (in descending order by the atoms count) where the number of components is less or equal to the limit number parameter
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

: The same as input, plus the columns with the connected components

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Workflows

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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: 2026-01-05

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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