cmf_fval_xyz: Computes field value at point (x,y,z)

In conmolfields: Continuous molecular fields

Description

Computes field value at point (x,y,z)

Usage

cmf_fval_xyz(ft, mol, alpha, x, y, z)

Arguments

ft
mol
alpha
x
y
z

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_fval_xyz <- function(ft, mol, alpha, x, y, z) {
  fval <- 0.0
  natoms <- length(mol$atoms)
  for (iatom in 1:natoms) {
    atom <- mol$atoms[[iatom]]
    dist2 <- (x - atom$x)^2 + (y - atom$y)^2 + (z - atom$z)^2
	if (ft == "q") {
      fval <- fval + atom$pch * exp(- alpha * dist2 / 2.0)
	} else if (ft == "vdw") {
      dist2rel <- dist2 / (tripos_Rvdw[[atom$syb]])^2
      fval <- fval + tripos_Evdw[[atom$syb]] * exp(- alpha * dist2rel / 2.0)
	} else if (ft == "logp") {
      fval <- fval + atom$hydroph * exp(- alpha * dist2 / 2.0)
	} else if (ft == "abra") {
      fval <- fval + atom$abraham_a * exp(- alpha * dist2 / 2.0)
	} else if (ft == "abrb") {
      fval <- fval + atom$abraham_b * exp(- alpha * dist2 / 2.0)
    } else if (ft == "mop_q") {
      fval <- fval + atom$mop_q * exp(- alpha * dist2 / 2.0)
    } else if (ft == "mop_dn") {
      fval <- fval + atom$mop_dn * exp(- alpha * dist2 / 2.0)
    } else if (ft == "mop_de") {
      fval <- fval + atom$mop_de * exp(- alpha * dist2 / 2.0)
    } else if (ft == "mop_pis") {
      fval <- fval + atom$mop_pis * exp(- alpha * dist2 / 2.0)
    } else if (ft == "mop_homo") {
      fval <- fval + atom$mop_homo * exp(- alpha * dist2 / 2.0)
    } else if (ft == "mop_lumo") {
      fval <- fval + atom$mop_lumo * exp(- alpha * dist2 / 2.0)
	} else if (ft == "ind") {
      fval <- fval + exp(- alpha * dist2 / 2.0)
	} else if (ft %in% tripos_atom_types) {
	  if (ft == atom$syb) {
        fval <- fval + exp(- alpha * dist2 / 2.0)
	  }
	}
  }
  fval
}

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