A number of distance metrics can be calculated for binary fingerprints. Some of these are actually similarity metrics and thus represent the reverse of a distance metric.
The following are distance (dissimilarity) metrics
Hamming
Mean Hamming
Soergel
Pattern Difference
Variance
Size
Shape
The following metrics are similarity metrics and so the distance can be obtained by subtracting the value fom 1.0
Tanimoto
Dice
Modified Tanimoto
Simple
Jaccard
RusselRao
Rodgers Tanimoto
Cosine
Achiai
Carbo
Baroniurbanibuser
Kulczynski2
Finally the method also provides a set of composite and asymmetric distance metrics
Hamann
Yule
Pearson
Dispersion
McConnaughey
Stiles
Simpson
Petke
The default metric is the Tanimoto coefficient.
1  distance(fp1, fp2, method)

fp1 
An object of class 
fp2 
An object of class 
method 
The type of distance metric desired. Partial matching is
supported and the deault is

Numeric value representing the distance in the specified metric between the supplied fingerprint objects
Rajarshi Guha rguha@indiana.edu
Fligner, M.A.; Verducci, J.S.; Blower, P.E.; A Modification of the JaccardTanimoto Similarity Index for Diverse Selection of Chemical Compounds Using Binary Strings, Technometrics, 2002, 44(2), 110119
Monve, V.; Introduction to Similarity Searching in Chemistry, MATCH  Comm. Math. Comp. Chem., 2004, 51, 738
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