On Wed, Sep 30, 2015 at 8:05 AM, Guillaume GODIN < guillaume.go...@firmenich.com> wrote:
> > > When you say as closely as I could, do you mean that all the paramaters > are the sames in ECFP and Morgan but the only divergence between them is on > the way RDKit/Pipeline handle aromaticity + hashing ? > I don't think that there are any parameters. I followed the algorithm description in the paper, but since the fingerprints include information about chemistry (specifically about bond types, which include aromaticity), differences could arise. The hashing algorithm is not described in the paper, so that will definitely be different. The Morgan fingerprints in the RDKit will not produce the same fingerprint as PP's ECFP implementation, but they should produce very similar similarity values (as the presentation I referenced earlier demonstrates). Best, -greg
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