Computes CMF kernel matrices for training and saves to file
comp_kernels_train(train_fname = "ligands-train.mol2", kernels_train_fname = "ligands-kernels-train.RData", mfields = c("q", "vdw", "logp", "abra", "abrb"), print_comp_kernels = TRUE, ...)
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kernels_train_fname | |
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##---- Should be DIRECTLY executable !! ---- ##-- ==> Define data, use random, ##-- or do help(data=index) for the standard data sets. ## The function is currently defined as function (train_fname = "ligands-train.mol2", kernels_train_fname = "ligands-kernels-train.RData", mfields = c("q", "vdw", "logp", "abra", "abrb"), print_comp_kernels = TRUE, ...) { mdb0 <- read_mol2(train_fname) mdb <- cmf_params_tripos(mdb0) nfields <- length(mfields) syb_types <- get_syb_types_list(mdb) kernels <- list() kernels$alphas <- alphas for (f in 1:nfields) { kernels[[mfields[f]]] <- list() } for (ialpha in 1:length(alphas)) { alpha <- alphas[ialpha] for (f in 1:nfields) { field <- mfields[f] if (print_comp_kernels) { cat(sprintf("computing kernel_%s for alpha=%g\n", field, alpha)) flush.console() } if (field == "ind") { Km <- 0 for (type in syb_types) { if (print_comp_kernels) cat(type) Km <- Km + cmf_indicator_kernel_matrix(mdb, alpha, type, verbose = print_comp_kernels) } } else { Km <- cmf_kernel_matrix_tt(field, mdb, alpha, verbose = print_comp_kernels) } kernels[[field]][[ialpha]] <- Km } } save(kernels, file = kernels_train_fname) }#> function (train_fname = "ligands-train.mol2", kernels_train_fname = "ligands-kernels-train.RData", #> mfields = c("q", "vdw", "logp", "abra", "abrb"), print_comp_kernels = TRUE, #> ...) #> { #> mdb0 <- read_mol2(train_fname) #> mdb <- cmf_params_tripos(mdb0) #> nfields <- length(mfields) #> syb_types <- get_syb_types_list(mdb) #> kernels <- list() #> kernels$alphas <- alphas #> for (f in 1:nfields) { #> kernels[[mfields[f]]] <- list() #> } #> for (ialpha in 1:length(alphas)) { #> alpha <- alphas[ialpha] #> for (f in 1:nfields) { #> field <- mfields[f] #> if (print_comp_kernels) { #> cat(sprintf("computing kernel_%s for alpha=%g\n", #> field, alpha)) #> flush.console() #> } #> if (field == "ind") { #> Km <- 0 #> for (type in syb_types) { #> if (print_comp_kernels) #> cat(type) #> Km <- Km + cmf_indicator_kernel_matrix(mdb, #> alpha, type, verbose = print_comp_kernels) #> } #> } #> else { #> Km <- cmf_kernel_matrix_tt(field, mdb, alpha, #> verbose = print_comp_kernels) #> } #> kernels[[field]][[ialpha]] <- Km #> } #> } #> save(kernels, file = kernels_train_fname) #> } #> <environment: 0x10b466790>