0 ×

RDKit Molecule Catalog Filter

RDKit Nodes for Knime version 4.0.1.v202006261025 by NIBR

Filters a table of molecules by applying filters taken from a set of standard catalogs. The second output table contains a very detailed view of the reasons why a molecule was filtered out. The node gives the option to generate one or more atom lists columns with the indexes of the atoms that matched the rule; this information can be used with the RDKit Molecule Highlighting node to color the associated substructures.


RDKit Mol column
The input column with RDKit Molecules.
Filter catalogs to apply
Define which filter catalogs shall be used for filtering.
Prefix for result columns
Column names for the second (filtered out) table are automatically assigned, but a prefix can be assigned, which makes it possible to run this node sub-sequentially with different filters.
Atom list handling
Controls whether or not lists of atoms matching the filters are generated. This also controls whether all matching atoms are in a single list or if there is a column per filter catalog.

Input Ports

Input table with RDKit Molecules to be filtered

Output Ports

Molecules which have not been filtered out
Molecules which have been filtered out and associated reasons

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.

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.


You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.