gistfile1.r

library(rcdk)

## Compare methods to convert Java BitSet -> R vector

mol <- parse.smiles("O=C(OC)C(c1ccccc1)C2NCCCC2")
fp <- .jnew('org/openscience/cdk/fingerprint/Fingerprinter',
            as.integer(1024),
            as.integer(6))
bitset <- .jcall(fp, "Ljava/util/BitSet;", "getFingerprint", mol)

system.time(
            sapply(1:100, function(i) {
              bitset <- .jcall(bitset, "S", "toString")
              s <- gsub('[{}]','', bitset)
              s <- as.numeric(strsplit(s, split=',')[[1]])-1
            }))

system.time(
            sapply(1:100, function(i) {
              nbit <- 1024
              bitvals <- sapply(1:nbit, function(x) {
                .jcall(bitset, "Z", "get", as.integer(x-1))
              })
              bitvals <- which(bitvals)-1
            }))