CDK to Molecule

Converts the CDK molecules in one of the input table's columns into various string representations (SDF, Mol2, Smiles, CML).

This node uses CDK classes to parse and display structures.

Options

CDK Column
The column that contains the CDK molecules.
Replace Column
Select this to replace the CDK column with the column containing the converted string representations. 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).
Destination format
Select the destination format here.

Input Ports

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Table containing CDK molecules

Output Ports

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Table with the molecules' converted string representations

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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:

v4.7
Plugin provider: KNIME GmbH, Konstanz and EMBL-EBI, Cambridge
Plugin version: 1.5.700.v202211291308
On NodePit since: 2022-12-06
Last update: 2022-12-07
KNIME versions: Since v3.6