cmf_gen_grid_ex: Generation of grid for continuous molecular co-fields...

In conmolfields: Continuous molecular fields

Description

Generation of grid for continuous molecular co-fields Extended version with field families

Usage

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, ...)

Arguments

train_fname
kernels_fname
model_fname
grid_fname
field_family
verbose
...

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", 
    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)
  }

conmolfields documentation built on May 2, 2019, 4:18 p.m.