Hey Greg,
thank you for your reply.
Am 17.11.2016 um 06:27 schrieb Greg Landrum:
Hi Shanthy,
On Wed, Nov 16, 2016 at 9:07 AM, Shantheya Balasupramaniam
<s.balasupraman...@tu-bs.de <mailto: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?
When I went through the RDKit Documentation I noticed that the default
similarity metric used by DataStructs.FingerprintSimilarity() is
Tanimoto and the examples for the Morgan Fingerprint incorporate Dice...
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. :-)
That's exactly the answer I hoped for :)
-greg
Cheers,
Shanthy
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