Dear RDKit community, I was treating AllChem.GetMorganFingerprint(m1,2) the same as ECFP4. I am writing a paper for a open source tool, so I need to be very accurate. I have seen one open source implementation for ECFP, which is from CDK. Most researchers are using Pipeline Pilot to calculate ECFP. But, Pipeline Pilot is not open source.
I calculate taminoto similarity based on Morgan fingerprint. The similarity matrix is the input for my tool. I am wondering how different it is for Morgan fingerprint and ECFP. Will they give different answers in some situations? Can we use MorganFingerprint instead of ECFP most of the time? Thanks, Jing
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