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.
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
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