Hi Shanthy, On Wed, Nov 16, 2016 at 9:07 AM, Shantheya Balasupramaniam < s.balasupraman...@tu-bs.de> wrote:
> > as far as I' ve seen there are two possibilites to calculate MACCSKeys > Fingerprints with RDKit. > Is there a principle difference between Maccskeys.GenMACCSKeys() and > AllChem.GetMACCSKeysFingerprint()? > Since I calculated the fingerprints for a couple of molecules with both > options and the outcome was the same, I assume that it doesn't matter > which method is used? > Correct, the function in rdkit.Chem.MACCSkeys just calls the same C++ function that AllChem.GetMACCSKeysFingerprint() calls. It's still there for backwards compatibility reasons. > Furthermore the default similarity metric for the Topological > Fingerprints and MACCS Keys is set to Tanimoto while for the Morgan > Fingerprints Dice is used. > Where are you finding that default? > Is there a particular reason for the preference of the different > similarity metrics for the various Fingerprints? > Not really. I used to by default choose Dice when I was working with count-based fingerprints and Tanimoto when working with bit vectors. I no longer worry too much about that. Some people probably still have strong opinions on the matter; the RDKit supports whichever you prefer. :-) -greg
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