0 ×

RDKit Substructure Counter

RDKit Nodes for Knime version 4.2.0.v202103031419 by NIBR

This node is used to calculate the number of times a particular query molecule is present in an input molecule. The number of times the query molecule present in the input molecule can be repeated. It is possible to choose the unique number of times the query molecule is present in the input molecule.



RDKit Mol column
The input column with RDKit Molecules.
Input Query Column
The name of the column in second table containing query molecules which will act as substructure for the input molecules


Count Unique Matches Only?
This option is selected if user requires unique matches of the query molecule in an input molecule.
Use chirality
If this is set, information about stereochemistry will be used in the substructure search.


Instead of query molecules use names as result header titles (and tags)
Select this option to allow the node to use names specified in the query table as column title for the resulting count columns and tags. If disabled, it will use the SMILES or SMARTS value as title.
Column with names for header titles
If the last option is enabled the column with the query names must be selected here.
Add total hits count column
Select this option to add a column that contains the accumulated hits count of all hits.
New column name for total hits count
If the last option is enabled the name for the new column must be specified here.
Add column with tags for matching queries
Select this option to add a column that contains a collection of all tags (SMILES, SMARTS values or tags taken from header titles column) for the matching queries. This can be useful for further processing.
New column name for tags
If the last option is enabled the name for the new column must be specified here.

Input Ports

Table with input molecule column
Table with input query column

Output Ports

Input molecule table with one additional column for each row in the query molecule table. The new columns added contain the number of times that a query molecule is found in the molecule.


Interactive Table View
Displays the data in a table view. Has the capability to show chemical structures in the headers of the substructure count columns.

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.

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.