On Tue, Sep 29, 2015 at 8:22 PM, Jing Lu <ajin...@gmail.com> wrote: > > 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. >
To be very clear: the only implementation of ECFP is the one in Pipeline Pilot. The other implementations like the one in the CDK and the RDKit, may have followed the algorithm description that was published, but due to differences in aromaticity perception and hashing algorithms the results will not be exactly the same. > 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? > I have, in the past, done a comparison between similarity values calculated with the RDKit and those with PP's ECFP implementation. I've presented those results in a couple different places; here's one of them: http://rdkit.org/UGM/2012/Landrum_RDKit_UGM.Fingerprints.Final.pptx.pdf Best, -greg
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