Hi all,
I was trying to calculate a Similarity Matrix with Morgan Fingerprints
and TanimotoSimilarity.
If I use DataStructs.TanimotoSimilarity(fp,fp) I get a Simlarity of 1,
which I would expect. If I do the same with the
DataStructs.BulkTanimotoSimilarity(fps[i], fps[i]) i get a Similarity of
0, which actually is not a Similarity but a distance. I took this from
the cookbook (http://www.rdkit.org/docs/Cookbook.html) which states at
the clustering example:
# first generate the distance matrix:
dists = []
nfps = len(fps)
for i in range(1,nfps):
sims = DataStructs.BulkTanimotoSimilarity(fps[i],fps[:i])
dists.extend([1-x for x in sims])
Did I misunderstand something or is the dists list in the example
actually a list of Similarities, and the BulkTanimotoSimilarity actually
calculates the Tanimoto distance?
It would be great to get some clarification.
Thank you in advance,
Jennifer
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