利賓斯基規則篩選小分子

#======================================================= #======================================================= rm(list=ls()) library(ChemmineR) library(BioMedR) dt <- data.frame(name=c(1:1604), smie =c(1:1604)) sdfset <- read.SDFset("drug_fda.sdf") for (i in 1:1604) { smiles <- sdf2smiles(sdfset[i]) smiles <- smiles@smilist dt$smie[i] <- smiles } dt$smie <- as.character( dt$smie) setwd("D:\\SCIwork\\F41\\IFI44") mols = readMolFromSDF("drug_fda.sdf") dat = extrDrugRuleOfFive(mols) head(dat) dat$name <- rownames(dat) data_rule <- merge(dat, dt, by="name") write.csv(data_rule, file = "data_rule.csv") data_rule <- subset(data_rule, data_rule$LipinskiFailures == 0 ) # # write.csv(data_rule, file = "data_rule1.csv") drug <- read.csv("fda.csv", header = T) names(drug)[2] <- 'smie' data_rule <- merge(drug,data_rule, by="smie") vs <- read.csv("virtualscreening.csv", header = T) vs <- subset(vs, select = c("Ligand" , "Binding.Energy")) names(vs)[1] <- 'zinc_id' comdata <- merge(vs, data_rule, by="zinc_id") write.csv(comdata, file = "comdata.csv")