cmf_coef_xyz_sv: Computes coefficient at point (x,y,z) using support vectors

In conmolfields: Continuous molecular fields

Description

Computes coefficient at point (x,y,z) using support vectors

Usage

cmf_coef_xyz_sv(mdb, a, ai, alpha, x, y, z, field)

Arguments

mdb
a
ai
alpha
x
y
z
field

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
cmf_coef_xyz_sv <- function(mdb, a, ai, alpha, x, y, z, field) {
  coef <- 0.0
  nsv <- length(ai)
  for (isv in 1:nsv) {
    imol <- ai[isv]
	mol <- mdb[[imol]]
    natoms <- length(mol$atoms)
   for (iatom in 1:natoms) {
      atom <- mol$atoms[[iatom]]
      dist2 <- (x - atom$x)^2 + (y - atom$y)^2 + (z - atom$z)^2
	  if (field == "q") {
        coef <- coef + a[isv] * atom$pch * exp(- alpha * dist2 / 2.0)
	  } else if (field == "vdw") {
        dist2rel <- dist2 / (tripos_Rvdw[[atom$syb]])^2
        coef <- coef + a[isv] * tripos_Evdw[[atom$syb]] * exp(- alpha * dist2rel / 2.0)
	  } else if (field == "logp") {
        coef <- coef + a[isv] * atom$hydroph * exp(- alpha * dist2 / 2.0)
	  } else if (field == "abra") {
        coef <- coef + a[isv] * atom$abraham_a * exp(- alpha * dist2 / 2.0)
	  } else if (field == "abrb") {
        coef <- coef + a[isv] * atom$abraham_b * exp(- alpha * dist2 / 2.0)
	  } else if (field == "vdwr") {
        coef <- coef + a[isv] * tripos_Rvdw[[atom$syb]] * exp(- alpha * dist2 / 2.0)
	  } else if (field == "abrs") {
        coef <- coef + a[isv] * atom$abraham_s * exp(- alpha * dist2 / 2.0)
	  } else if (field == "abre") {
        coef <- coef + a[isv] * atom$abraham_e * exp(- alpha * dist2 / 2.0)
	  } else if (field == "mop_q") {
        coef <- coef + a[isv] * atom$mop_q * exp(- alpha * dist2 / 2.0)
	  } else if (field == "mop_dn") {
        coef <- coef + a[isv] * atom$mop_dn * exp(- alpha * dist2 / 2.0)
	  } else if (field == "mop_de") {
        coef <- coef + a[isv] * atom$mop_de * exp(- alpha * dist2 / 2.0)
	  } else if (field == "mop_pis") {
        coef <- coef + a[isv] * atom$mop_pis * exp(- alpha * dist2 / 2.0)
	  } else if (field == "mop_homo") {
        coef <- coef + a[isv] * atom$mop_homo * exp(- alpha * dist2 / 2.0)
	  } else if (field == "mop_lumo") {
        coef <- coef + a[isv] * atom$mop_lumo * exp(- alpha * dist2 / 2.0)
	  } else if (field == "ind") {
        coef <- coef + a[isv] * exp(- alpha * dist2 / 2.0)
	  } else if (field %in% tripos_atom_types) {
	    if (atom$syb == field) {
          coef <- coef + a[isv] * exp(- alpha * dist2 / 2.0)
		}
	  }
    }
  }
  coef
}

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