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rajarshi/simsearch.R

Created January 14, 2022 21:55
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simsearch.R
library(rcdk)
library(fingerprint)
query_smi <- "CCCCCCCC"
hmdb <- load.molecules("smpdb_structures/compounds-1.sdf")
junk <- lapply(hmdb, function(x) set.title(x, get.property(x, "DATABASE_ID")))
query_fp <- get.fingerprint(parse.smiles(query_smi)[[1]])
hmdb_fp <- lapply(hmdb, get.fingerprint)
sm <- fp.sim.matrix(hmdb_fp, list(query_fp))
rownames(sm) <- sapply(hmdb, get.property, "DATABASE_ID")
sm[ which.max(sm[,1]), ]
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