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RDKit Functional Group Filter

RDKit Nodes for Knime version 4.0.1.v202006261025 by NIBR

This node can be used for filtering sets of molecules based on named substructures (functional groups based on SMARTS). Note that the default definitions are constructed to try and define functional groups relevant for reactivity; consequently groups like -CF3 do not match the halogen pattern.


RDKit Mol column
It specifies which column contains the set of RDKit molecules.
Functional group definition file
File containing functional group definitions. This input is optional. Alternatively you may press "Load Defaults" to use default functional group definitions. Pressing the info button on the very right shows the content of the currently selected definitions incl. all SMARTS that describe the functional groups.
List of functional group filters
Defines the conditions for filtering molecules. Select the ones that needs to be applied on the molecules. If no filter pattern is selected, molecules are sent to the matching output table.
Recording of first non-matching pattern in new column
If checked, an additional column (the name can be specified) containing the first non-matching pattern is added to the table of failing molecules.

Input Ports

Table containing a set of RDKit molecules.

Output Ports

Table containing molecules that pass the filter.
Table containing molecules that do not pass the filter.

Best Friends (Incoming)

Best Friends (Outgoing)



To use this node in KNIME, install RDKit KNIME JUnit Test from the following update site:


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

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