Generation of grid for continuous molecular co-fields

cmf_gen_grid(train_fname = "ligands-train.mol2", kernels_fname = "ligands-kernels.RData", model_fname = "ligands-model.RData", grid_fname = "ligands-grid-krr.RData", verbose = TRUE, ...)

Arguments

train_fname

kernels_fname

model_fname

grid_fname

verbose

Details

Value

References

Note

See also

Examples

##---- 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", verbose = TRUE, ...) { load(kernels_fname) load(model_fname) mfields <- names(model$h) nfields <- length(mfields) mdb <- read_mol2(train_fname) mdb <- cmf_params_tripos(mdb) grid <- cmf_init_grid(mdb) grids <- list() for (f in 1:nfields) { field <- mfields[f] if (verbose) { cat(sprintf("Generating grid for field %s...\n", field)) flush.console() } grids[[field]] <- cmf_coef_grid(mdb, model$a, model$alpha[[field]], grid, field) } save(grids, file = grid_fname) }
#> function (train_fname = "ligands-train.mol2", kernels_fname = "ligands-kernels.RData", #> model_fname = "ligands-model.RData", grid_fname = "ligands-grid-krr.RData", #> verbose = TRUE, ...) #> { #> load(kernels_fname) #> load(model_fname) #> mfields <- names(model$h) #> nfields <- length(mfields) #> mdb <- read_mol2(train_fname) #> 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(mdb, model$a, model$alpha[[field]], #> grid, field) #> } #> save(grids, file = grid_fname) #> } #> <environment: 0x10e61a8b0>