Organic Splitter

This node accepts a table with Indigo molecules and splits it into three sets, one with all organic rows, the second with all the rest, the last one gather all the rows with invalid data (with data which cannot be translated into indigo object for some reasons).

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 molecules.
Interpret alkali metal salts as inorganic molecules
Conditions defining whether consider alkali metal salts as an organic or not. Yes, by default.
Interpret molecules containing d-block elements as inorganic molecules
Conditions defining whether consider molecules containing d-block elements as an organic or not. Yes, by default.
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

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Table containing molecules.

Output Ports

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Rows with organic molecules.
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Rows with inorganic molecules.
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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: 2026-01-22
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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