#glgfilemarker.R makes GLG file and map files

#!/usr/bin/env Rscript      
args = commandArgs(trailingOnly=TRUE) 

if(length(args) < 1){
  stop("USE: Rscript glgfilemaker.R <receptor_name> <session_dir>") 
}

#Arguments definition 
receptor_name <- args[1] 
session_dir <- args[2]

#Running AutiGrid4
##autogrid4 -p <file>.gpf -l <file>.glg &


recopy <- paste( basename(args[1]),".pdbqt" ,sep="") 
command <- paste("cp ", args[1], " ", recopy, sep="")
#print(paste("ESTOY IMPRIMIENDO ", command))
system(command)

#print(recopy)

receptor_name_gpf <- paste( basename(args[1]), ".gpf", sep="")
receptor_name_glg <- paste( basename(args[1]), ".glg", sep="")
#print(receptor_name_gpf)
elemento_concetenar <- paste( "autogrid4 -p", sep = " ")
elemento_concetenar <- paste(elemento_concetenar, receptor_name_gpf, sep = " ")
elemento_concetenar <- paste(elemento_concetenar, "-l ", receptor_name_glg, sep = " ")

#print(elemento_concetenar)


system(elemento_concetenar)