molecule3d04.r

#################################
# ball and stick model
#################################

# get bond info
bonds       <- get.bonds(molfile)
bonds.atoms <- data.frame(do.call('rbind', lapply(bonds, function(x){
  atoms <- get.atoms(x)
  start <- get.point3d(atoms[[1]])
  end   <- get.point3d(atoms[[2]])
  return (list(start.x = start[1], start.y = start[2], start.z = start[3],
                 end.x =   end[1],   end.y =   end[2],   end.z =   end[3]))
})))

# open rgl device
open3d()

# plot sticks
mapply(function(x1, y1, z1, x2, y2, z2){
  shade3d(cylinder3d(data.frame(x = c(x1, x2), y = c(y1, y2), z = c(z1, z2)),
                     radius = 0.1, sides = 16,
                     e2=rbind(c(1,0,0),c(1,0,0))), col="grey")
}, bonds.atoms$start.x, bonds.atoms$start.y, bonds.atoms$start.z,
   bonds.atoms$end.x,   bonds.atoms$end.y,   bonds.atoms$end.z)

# plot balls
mapply(function(x, y, z, vdw, col){
  spheres3d(x, y, z, vdw*0.25, col = col, add = T)
}, atom_dat$x, atom_dat$y, atom_dat$z,
atom_dat$vanderwaals, atom_dat$colour)