Well many of you ,who are using r for cheminformatics must be knowing rcdk . Regarding the tanimoto calculation i have seen it seem it takes a long time to calculate the code in rcdk code looks neat but still the similarity calculation can be performed much faster using the inner products.Below given a simple code to do that and also the time taken is like 10 times faster than the rcdk code. Quite an impressive performance boost . I have made a pull request to Rajarshi's code, it should be available soon in the main package.
Time taken for the new method
#Normal method in rcdk
##Consider m is the binary matrix of 0 and 1 which you calculated using fp.sim.matrix###
user system elapsed
2.962 0.012 2.971
#Normal method in rcdk
user system elapsed
43.644 0.064 43.707
