cmf_aa_kernel: Computation of the kernel that compares fields of two atoms

In conmolfields: Continuous molecular fields

Description

Computation of the kernel that compares fields of two atoms

Usage

cmf_aa_kernel(ft, atom1, atom2, alpha)

Arguments

ft
atom1
atom2
alpha

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(ft, atom1, atom2, alpha) {
  dist2 <- eucldist2(atom1, atom2)
  val <- 0.0
  if (ft == "q") {
    val <- atom1$pch * atom2$pch * exp(- alpha * dist2 / 4.0)
  } else if (ft == "vdwr") {
    val <- tripos_Rvdw[[atom1$syb]] * tripos_Rvdw[[atom2$syb]] * exp(- alpha * dist2 / 4.0)
  } else if (ft == "vdw") {
    w1 <- tripos_Evdw[[atom1$syb]]
    w2 <- tripos_Evdw[[atom2$syb]]
    a1 <- alpha / tripos_Rvdw[[atom1$syb]]^2
    a2 <- alpha / tripos_Rvdw[[atom2$syb]]^2
    coef <- (4 * sqrt(pi^3)) / ((a1+a2) * sqrt(2*a1+2*a2))
    expart <- exp( - (a1*a2*dist2) / (2 * (a1+a2)) )
    val <- w1 * w2 * coef * expart
  } else if (ft == "logp") {
    val <- atom1$hydroph * atom2$hydroph * exp(- alpha * dist2 / 4.0)
  } else if (ft == "abra") {
    val <- atom1$abraham_a * atom2$abraham_a * exp(- alpha * dist2 / 4.0)
  } else if (ft == "abrb") {
    val <- atom1$abraham_b * atom2$abraham_b * exp(- alpha * dist2 / 4.0)
  } else if (ft == "abrs") {
    val <- atom1$abraham_s * atom2$abraham_s * exp(- alpha * dist2 / 4.0)
  } else if (ft == "abre") {
    val <- atom1$abraham_e * atom2$abraham_e * exp(- alpha * dist2 / 4.0)
  } else if (ft == "mop_q") {
    val <- atom1$mop_q * atom2$mop_q * exp(- alpha * dist2 / 4.0)
  } else if (ft == "mop_dn") {
    val <- atom1$mop_dn * atom2$mop_dn * exp(- alpha * dist2 / 4.0)
  } else if (ft == "mop_de") {
    val <- atom1$mop_de * atom2$mop_de * exp(- alpha * dist2 / 4.0)
  } else if (ft == "mop_pis") {
    val <- atom1$mop_pis * atom2$mop_pis * exp(- alpha * dist2 / 4.0)
  } else if (ft == "mop_homo") {
    val <- atom1$mop_homo * atom2$mop_homo * exp(- alpha * dist2 / 4.0)
  } else if (ft == "mop_lumo") {
    val <- atom1$mop_lumo * atom2$mop_lumo * exp(- alpha * dist2 / 4.0)
  } else if (ft == "ind") {
    if (atom1$syb == atom2$syb) {
      val <- exp(- alpha * dist2 / 4.0)
	}
  }
  if (ft != "vdw") {
    val <- val * sqrt(pi^3 / alpha^3)
  }
  val
}

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