I have a text file containing 100 drug compounds (rows) and 100 protein kinase targets (columns). Values reflect how tightly a compound binds to a target. I also have the drug SMILES of the drugs.
I converted SMILES to SDF. Then I used "fingerprintOB" function to generate fingerprints from that SDFset using OpenBabel. I generated 3 different fingerprints, i.e. FP2, FP3, FP4
Now using those fingerprints, I want to compute fingerprint-based Tanimoto kernels.
Which function should I use? fpSim? Or cmp.similarity?
cmp.similarity does not work.. It asks for apset data, but I have no idea how to convert FPsets (i.e. FP2, FP3, FP4) to apset data..