Hydrogen Manipulator

This node adds missing hydrogens to CDK molecules and forces all hydrogens to be implicit. Stereochemistry is converted onto non-terminal bonds.

Options

Column with molecules: Select the column containing the molecular structure.
Exclude 'stereo hydrogens': Whether stereo-relevant hydrogens should be kept.
Append Column: Appends a new molecule column (with the name as specified in the text field) if checked, replaces the original column otherwise.

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To use this node in KNIME, install the extension KNIME-CDK from the below update site following our NodePit Product and Node Installation Guide:

v5.9

Plugin provider: KNIME GmbH, Konstanz and EMBL-EBI, Cambridge

Plugin version: 1.5.700.v202511141653

On NodePit since: 2025-12-11

Last update: 2026-01-21

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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