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KNIME CDK Integration version 1.5.700.v202006231106 by KNIME GmbH, Konstanz and EMBL-EBI, Cambridge

This node lets you handle unconnected CDK molecules. This is necessary because some algorithms won't work with unconnected structures. You have the choice to completely remove the compounds that contain unconnected molecules, remove all molecule parts except the biggest one, or keep all fragments as separate molecules.


Column with molecules
Select the column containing the molecular structure
Remove complete row
Replaces the cell that contains a molecule with multiple fragments by a missing data cell
Leave biggest fragment
Removes all fragments except the biggest from unconnected molecules
Add column with all fragments
Adds a collection column that contains all fragments a molecule consists of

Input Ports

Table containing molecular structures

Output Ports

As input but without unconnected molecules

Best Friends (Incoming)

Best Friends (Outgoing)



To use this node in KNIME, install KNIME-CDK from the following update site:


A zipped version of the software site can be downloaded here.

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