molecule3d02.r

# create a data.frame with atom properties
atom.props <- data.frame(
  symbol      = c("O", "N", "C", "H"),
  vanderwaals = c(1.52, 1.55, 1.7, 1.2), #Van der Waals radii of atoms
  colour      = c("red", "blue", grey(0.1), "white")
)

# get atoms from the molecule
atoms <- get.atoms(molfile)

# get 3D locations of atoms as read from the file
atom_dat        <- data.frame(do.call('rbind', lapply(atoms, get.point3d)))
names(atom_dat) <- c("x", "y", "z")

# merge with atom info
atom_dat$symbol <- unlist(lapply(atoms, get.symbol))
atom_dat        <- merge(atom_dat, atom.props, all.x = T, all.y = F)