I am running a similarity search process using rdkit where my query consists of ~20 templates and my target consists of ~1000 molecules. How can I create a list (or any container) of molecules that I can iterate later.

My present algorithm is

read template create molecule > read target create molecule > calculate similarity
go back to template and follow the same process

But by doing this I am creating same molecule multiple times, which is increasing the run time.

Thank in advance for any helps.

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