cmf_gen_grid_ex {conmolfields} | R Documentation |
Generation of grid for continuous molecular co-fields
Extended version with field families
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)
}
[Package
conmolfields version 0.0-19
Index]