R/plot_molecule.R

In ceparman/mongochem:

plot_molecule <- function(molecule, name = NULL, sma = NULL, ...){
#' molecule an object as returned by rcdk::load.molecules or rcdk::parse.smiles()
#' name a character for the name of the molecule,
#' sma a character witht the smarts string as passed onto get.depictor()
#' ... other arguments for get.depictor()
#' Addition parameter
#' annotate= "number", plot atom numbers
#' supressh = T, plot Hydrogens
#'@export
  # Image aesthetics
  dep <- rcdk::get.depictor(
    width = 1000, height = 1000,
    zoom = 7, sma = sma, ...
  )
  molecule_sdf <- rcdk::view.image.2d(molecule[[1]], depictor = dep)


  ## Remove extra margins around the molecule
  par(mar=c(0,0,0,0))
  plot(NA,
       xlim=c(1, 10), ylim=c(1, 10),
       # Remove the black bounding boxes around the molecule
       axes = F)
  rasterImage(molecule_sdf, 1,1, 10,10)
  # Annotate the molecule
  if(is.null(name)){
  text(x = 5.5, y = 1.1,  deparse(substitute(molecule)))
  } else{text(x = 5.5, y = 1.1,  name)


  }
}