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Substructure Search

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

This node allows to draw a fragment in the dialog. Upon execution the molecules from the input table are divided into two sets, one with all molecules that contain the fragments, the other with all molecules that do not contain it.

The substructure search matches stereochemistry if defined. The total number of matched substructures is limited to five.

The fragments are passed between JChemPaint and the CDK in SMILES format. Hence, if the fragment string is provided as flow variable, the input must be in SMILES format as well.


Use the control options to assemble a structure. If a previously drawn molecule does not show up when opening the dialog, you may need to scroll down the editor pane.
Column with molecules
Select the column that contains the molecules.
Match charges
Matches charges.
Exact match
Exact stereochemistry match: Undefined chiral centers in the query molecule must also be undefined in the target molecule.
Highlight substructure
Highlights all found substructures in the molecules.

Input Ports

Table that contains at least one column with CDK molecules.

Output Ports

Table with all molecules that contain the fragment.
Table with all molecules that do not contain the fragment.

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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