R/viewstr.R

In iqspr: Inverse Molecular Design

#'view 2D structures from SMILES string vector
#' @description View 2D structures from SMILES strings vector
#' @param smis is a SMILES strings vector to submit.
#' @param width of the picture
#' @param height of the picture
#' @param nrow is the number of rows for the table of molecular depictions
#' @param ncol is the number of columns for the table of molecular depictions
#' @param legend is the text to appear for each molecular depiction in the top left corner
#'
#' @examples viewstr(c("c1ccc2ccc3c(NCCN(C)C)cc(nc3c2c1)", "c1ccc2ccc3c(NCCN(CC)CCCl)cc(nc3c2c1)",
#'  "c1ccc2ccc3c(NC(CC)CC)cc(nc3c2c1)", "c1ccc2ccc3c(c2c1)ncc(c3NCCNCC=CCCCC)"))
#'
#' @return a plot of requested 2D structures.
#'
#' @importFrom graphics par
#' @importFrom utils packageVersion
#' @import rcdk
#'
#' @export viewstr

viewstr <- function(smis = NULL, width = 500, height = 500, nrow = 2, ncol = 2, legend = ""){
  par(mar = c(0,0,0,0))
  par(mfrow = c(nrow,ncol))
  smisl <- length(smis)
  for(i in 1:smisl){
    mol <- parse.smiles(as.character(smis[i]), kekulise = T)[[1]] # if kekulise = F, aromatic rings are missed!
    dep <- get.depictor(width=width, height=height, zoom=3)
    temp <- view.image.2d(molecule=mol,depictor=dep)
    plot(NA,NA,xlim=c(1,10),ylim=c(1,10),xaxt='n',yaxt='n',xlab='',ylab='')
    rasterImage(temp,1,1,10,10)
    legend("topleft", legend[i], bty = "n", cex = 1.3)
  }
}