# # # R代码从装饰图案的Rchemcpp来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:Rchemcpp。Rnw: 37-41 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #选项(宽度= 75)set.seed(0)图书馆(Rchemcpp) RchemcppVersion <——packageDescription (“Rchemcpp”)美元版本# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:Rchemcpp。Rnw: 97 - 98 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(Rchemcpp) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:Rchemcpp。Rnw: 105 - 108 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # sdfolder < -执行(“extdata”,包=“Rchemcpp”)自卫队< - list.files (sdfolder full.names = TRUE,模式=“小”)K <——sd2gram (sdf) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:Rchemcpp。Rnw: 114 - 115 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #的热图(K, Rowv = NA, Colv = NA,规模=“没有”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:Rchemcpp。Rnw: 119 - 122 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # pdf (“001. pdf”)的热图(K, Rowv = NA, Colv = NA,规模=“没有”,利润= c(12日12))dev.off() # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:Rchemcpp。Rnw: 141 - 143 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(apcluster) r <——apcluster (K) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:Rchemcpp。Rnw: 147 - 148 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #的热图(r, K) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:Rchemcpp。Rnw: 151 - 154 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # pdf (“002. pdf”)的热图(r、K、利润率= c(12日12))dev.off() # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:Rchemcpp。Rnw: 173 - 182 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(kernlab) chromosomeAberrationDataSet < -列表。文件(sdfolder, full.names = TRUE,模式=“Mohr.sdf”)王者文化< - sd2gramSpectrum (chromosomeAberrationDataSet detectArom = FALSE, depthMax = 4, silentMode = TRUE)响应< - getMoleculePropertyFromSDF (chromosomeAberrationDataSet, chromosome_damage) # 0.1 C将运算速度,应该设置为较高的值模型<——ksvm(王者文化,y = as.factor(反应),内核=“矩阵”,交叉= 10,类型=“C-svc”, C = 0.1) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块10号:Rchemcpp。Rnw: 186 - 187 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #打印(1-model@cross) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块11号:Rchemcpp。Rnw: 192 - 193 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #预测(模型、as.kernelMatrix(王者文化[3,SVindex(模型),下降= FALSE))) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块12号:Rchemcpp。Rnw: 202 - 206 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(ChemmineR) sdfFileName < - list.files (sdfolder full.names = TRUE,模式=“小”)sdfSet <——read.SDFset (sdfFileName)情节(sdfSet[2],打印= FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块13号:Rchemcpp。Rnw: 210 - 211 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # K1 <——sd2gramSubtree (sdfSet silentMode = TRUE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块14号:Rchemcpp。Rnw: 218 - 221 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # leadCompound < - sdfSet [1] compoundDataBase < - sdfSet [1:20] K2 <——sd2gramSubtree (leadCompound、compoundDataBase silentMode = TRUE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量15:Rchemcpp。Rnw: 471 - 472 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # toBibtex(引用(“Rchemcpp”))