Hello,

I have the following problem:

Given two SD files a.sdf and b.sdf. Each SD file contains around 1 million molecules. Now, I would like calculate similarities between pairs of molecules.

For instance, similarity between first molecule from a.sdf and first molecule from b.sdf, second molecule from a.sdf and second molecule from b.sdf, etc.

until last molecule from a.sdf and last molecule from b.sdf.

What is the fastest way in Pipeline Pilot to calculate these similarities between pairs of molecules?

Many thanks for your answers,

Torsten