Similarity matrix (Tanimoto)

I am an intermediate KNIME user and I have a little trouble with my workflow

I need a node that can give me the similarity Tanimoto co-efficient of over 200 compounds in a matrix form.
I found a node developed by Schrodingen named “Similarity Matrix (from molecules)”, but it kept failing to execute with this error message “Execute failed: Licence is not correctly set”

I don’t know if anyone can advise me with a compatible node for my workflow.



Hi @adesinoh and welcome to the KNIME community !

Below you will find a workflow which provides a full Tanimoto matrix distance:

20220216 Pikairos Tanimoto Similarity Matrix.knwf (110.1 KB)

The extra work needed here was to transform a Half-Diagonal Distance matrix provided by the -Distance Matrix Calculate- node into a full Distance Matrix with “Ones” diagonal included.
This can be generalized to a Euclidean Distance Matrix where the diagonal should be made of Zeros.

Hope it helps.

Best wishes,



Hi @adesinoh
The nodes you tried come from the Schroedinger suite and they require a license. That’s why you get an error. Do you already use the Schroedinger suite? Here is info on obtaining and installing the license for Schroedinger products.
Btw, @aworker has proposed a nice way to calculate the pairwise Tanimoto coefficients with the open source RDKit and native KNIME nodes.



Thank you for this reply, it has resolved my little trouble :smile:


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