Molecule to CDK

Converts the elements in one of the input table's columns into an internal format (CDKCell), which can then be rendered as molecule or used for further computations. The target column must contain string representations of molecules (SDF, Mol2, SMILES [no stereo information], CML, InChI).

For on untyped InChI or SMILES string, the line notation is inferred. If the string starts with "InChI=", the InChI parser is used, the SMILES parser otherwise. The option's dialog will not automatically select an input column as a string cell may not contain the right input, in contrast to typed SDF, Mol2, or SMILES cells.

This node uses CDK classes to parse and display structures.

Options

Molecule Column: The column that contains the molecules.
Replace Column: Select this to replace the molecule column with the column containing the converted CDK molecules. Otherwise a new column will be appended.
New column name: Enter the name of the new column here if the original column is not replaced (see option above).
Generate 2D coordinates: Enabling this option will generate 2D coordinates for the converted molecules so that they can be visualized.
Force 2D generation: Without this option, 2D coordinates will only be generated for molecules that do not only have any (usually detected by an all zero z-coordinate). If this options is enabled the coordinates will be generated in any case.
Kekulize: An experimental feature that tries to infer double bonds in an aromatic system if not given by the input file. E.g., when the bond order in a SDFile is used to indicate aromaticity (bond order 4).

Input Ports

: Table containing molecules to parse

Output Ports

: Table with the parsed molecules

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Installation

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: 2026-01-22

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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