Generation of grid for continuous molecular co-fields Extended version with field families
cmf_gen_grid_ex(train_fname = "ligands-train.mol2", kernels_fname = "ligands-kernels.RData", model_fname = "ligands-model.RData", grid_fname = "ligands-grid-krr.RData", field_family = "PHCH", verbose = 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", kernels_fname = "ligands-kernels.RData", model_fname = "ligands-model.RData", grid_fname = "ligands-grid-krr.RData", field_family = "PHCH", verbose = TRUE, ...) { load(kernels_fname) load(model_fname) mfields <- names(model$h) nfields <- length(mfields) mdb <- read_mol2(train_fname) if (field_family == "PHCH") mdb <- cmf_params_tripos(mdb) grid <- cmf_init_grid(mdb) grids <- list() for (f in 1:nfields) { field <- mfields[f] if (verbose) { cat(sprintf("Generating grid for field %s...\n", field)) flush.console() } grids[[field]] <- cmf_coef_grid_ex(mdb, model$a, model$alpha[[field]], grid, field, field_family) } save(grids, file = grid_fname) }#> function (train_fname = "ligands-train.mol2", kernels_fname = "ligands-kernels.RData", #> model_fname = "ligands-model.RData", grid_fname = "ligands-grid-krr.RData", #> field_family = "PHCH", verbose = TRUE, ...) #> { #> load(kernels_fname) #> load(model_fname) #> mfields <- names(model$h) #> nfields <- length(mfields) #> mdb <- read_mol2(train_fname) #> if (field_family == "PHCH") #> mdb <- cmf_params_tripos(mdb) #> grid <- cmf_init_grid(mdb) #> grids <- list() #> for (f in 1:nfields) { #> field <- mfields[f] #> if (verbose) { #> cat(sprintf("Generating grid for field %s...\n", #> field)) #> flush.console() #> } #> grids[[field]] <- cmf_coef_grid_ex(mdb, model$a, model$alpha[[field]], #> grid, field, field_family) #> } #> save(grids, file = grid_fname) #> } #> <environment: 0x10ef5d6d8>