On Wed, Sep 30, 2015 at 6:47 AM, Greg Landrum <[email protected]> wrote:
> > On Tue, Sep 29, 2015 at 8:22 PM, Jing Lu <[email protected]> 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. > Sorry, should have been more explicit here: when I did the Morgan fingerprint implementation for the RDKit, I followed the published algorithm description as closely as I could. -greg
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