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RDKit Molecule Substructure Filter

RDKit Nodes for Knime version 4.2.0.v202103031419 by NIBR

Applies a substructure filter to an input RDKit Mol column. The patterns are given as SMARTS, SMILES, SDF or RDKit molecules in the second input table. You can choose either a minimum number of patterns to match or to require that all match.


RDKit Mol column
Select the column from the first input table that contains the RDKit molecules
Query Mol column
Select the column from the second input table that contains the query molecules. Acceptable types are SMARTS, SMILES, SDF and RDKit Mol.
Use chirality
If this is set, information about stereochemistry will be used in the substructure search.
Select the minimum number of patterns that must match for each molecule so that it is included in the first output table
New column name for matching substructures
Enter here the name of the new column that will contain a list of all matching substructure row indices


Fingerprint screening threshold
Substructure search performance can be improved using fingerprints. This makes sense when there are many different query molecules and a lot of input molecules. In this case the node can pre-calculate fingerprints once for all input and query molecules and do some pre-screening for substructure matching. The fingerprint screening threshold value defines the number of query molecules (table 2) that must be present in order to enable fingerprint calculation and pre-screening. Set it to 0 to disable fingerprint screening completely for this node. Set it to -1 to always use the RDKit Nodes default behavior (the standard setting).
Use row keys as substructure match information
The column for matching substructure indices contained (for historic reasons) the row index, which turned out not to be too useful. Click this flag to use row keys instead, which is today the default for new nodes.

Input Ports

Table with RDKit molecules
Table with SMARTS, SMILES, SDF or RDKit Mol molecules to use as queries

Output Ports

Molecules matching the substructure query
Molecules not matching the substructure query

Best Friends (Incoming)

Best Friends (Outgoing)



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


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

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