Computes indicator kernel matrices for prediction and saves to file
comp_ind_kernels_pred(train_fname = "ligands-train.mol2", pred_fname = "ligands-pred.mol2", ind_kernels_pred_fname = "ligands-ind-kernels-pred.RData", print_comp_kernels = TRUE, ...)
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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", pred_fname = "ligands-pred.mol2", ind_kernels_pred_fname = "ligands-ind-kernels-pred.RData", print_comp_kernels = TRUE, ...) { mdb0_train <- read_mol2(train_fname) mdb0_pred <- read_mol2(pred_fname) mdb_train <- cmf_params_tripos(mdb0_train) mdb_pred <- cmf_params_tripos(mdb0_pred) syb_types <- get_syb_types_list(mdb_train) kernels_pred <- list() kernels_pred$alphas <- alphas for (type in syb_types) { kernels_pred[[type]] <- list() } for (ialpha in 1:length(alphas)) { alpha <- alphas[ialpha] if (print_comp_kernels) { cat(sprintf("computing indicator kernels for alpha=%g\n", alpha)) flush.console() } for (type in syb_types) { if (print_comp_kernels) cat(type) kernels_pred[[type]][[ialpha]] <- cmf_indicator_kernel_matrix_pred(mdb_pred, mdb_train, alpha, type, verbose = print_comp_kernels) } } save(kernels_pred, file = ind_kernels_pred_fname) }#> function (train_fname = "ligands-train.mol2", pred_fname = "ligands-pred.mol2", #> ind_kernels_pred_fname = "ligands-ind-kernels-pred.RData", #> print_comp_kernels = TRUE, ...) #> { #> mdb0_train <- read_mol2(train_fname) #> mdb0_pred <- read_mol2(pred_fname) #> mdb_train <- cmf_params_tripos(mdb0_train) #> mdb_pred <- cmf_params_tripos(mdb0_pred) #> syb_types <- get_syb_types_list(mdb_train) #> kernels_pred <- list() #> kernels_pred$alphas <- alphas #> for (type in syb_types) { #> kernels_pred[[type]] <- list() #> } #> for (ialpha in 1:length(alphas)) { #> alpha <- alphas[ialpha] #> if (print_comp_kernels) { #> cat(sprintf("computing indicator kernels for alpha=%g\n", #> alpha)) #> flush.console() #> } #> for (type in syb_types) { #> if (print_comp_kernels) #> cat(type) #> kernels_pred[[type]][[ialpha]] <- cmf_indicator_kernel_matrix_pred(mdb_pred, #> mdb_train, alpha, type, verbose = print_comp_kernels) #> } #> } #> save(kernels_pred, file = ind_kernels_pred_fname) #> } #> <environment: 0x10de12240>