Description Usage Arguments Examples
Generation of grid for continuous molecular co-fields
1 | 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, ...)
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train_fname |
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kernels_fname |
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model_fname |
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grid_fname |
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verbose |
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... |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | ##---- 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)
}
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