cmf_kernel_matrix_tt: Computation of the kernel (Gram) matrix for the training set
In conmolfields: Continuous molecular fields

Computation of the kernel (Gram) matrix for the training set

1	cmf_kernel_matrix_tt(x)

x

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
cmf_kernel_matrix_tt <- function(ft, mdb, alpha, verbose=1) {
  nmol <- length(mdb)
  gram <- matrix(0, nmol, nmol)
  atomlists <- make_atom_lists(ft, mdb)
  for (imol in 1:nmol) {
    if (verbose) {cat("."); flush.console()}
    mol <- mdb[[imol]]
    gram[imol,imol] <- cmf_kernel_al(ft, mol, mol, alpha, atomlists[[imol]], atomlists[[imol]])
  }
  if (verbose) {cat("\n"); flush.console()}
  for (imol1 in 1:(nmol-1)) {
    mol1 <- mdb[[imol1]]
	if (verbose) {cat("."); flush.console()}
    for (imol2 in (imol1+1):nmol) {
      mol2 <- mdb[[imol2]]
      gram[imol1,imol2] <- cmf_kernel_al(ft, mol1, mol2, alpha, atomlists[[imol1]], atomlists[[imol2]])
      gram[imol2,imol1] <- gram[imol1,imol2]
    }
  }
}