#envelopesmaker.R makes FILL_Xout.pdb files  where X represents  values for envelopes from 10 to 100 

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

if(length(args) < 1){
  stop("USE: Rscript envelopesmaker.R <receptor_pdbqt> <session_dir> <pathAutoligand>")
}

#Arguments definition 
receptor_name <- args[1]
session_dir <- args[2]
pathLigand <- args[3]

#recopy <- paste("/home/galaxy/galaxy/tools/proteindocking/scripts/", basename(args[1]), ".txt", sep="")  
#command <- paste("cp ", args[1], " ", recopy, sep="") #18jun2018
#system(command) #18jun2018

#

recopy_2  <- scan(paste(basename(args[1]), ".txt", sep=""), what = character(), quiet = TRUE)


#print(paste("es lo que va a salir",recopy_2[1]))

#Ejecute from R a python script for Running Autoligand 
sizes_file <- scan("templateenvelopsizes.txt", what = character(), quiet = TRUE)

path_cajonDesastre <- recopy_2[1]

segment_paste <- paste("python", pathLigand, "-r", path_cajonDesastre, "-p", sep = " ")
#segment_paste <- paste("python /home/eugenia/workflowsoftware/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/AutoLigand.py -r", path_cajonDesastre, "-p", sep = " ")

#print(segment_paste)

#print(paste("es lo que va a salir",recopy_2[1]))

for(i in 1:length(sizes_file)){
size <- sizes_file[i]

##porcentaje <- (i/length(sizes_file))*100

##print(paste(paste(porcentaje, "%", sep = ""),"completed", sep = " "))


# HEMOS TACHADO ESTE SYSTEM
print(paste(segment_paste,size, sep = " ")) 

# ENABLE THIS SYSTEM
#system(paste(segment_paste,size, sep = " "), intern = TRUE) 
write(paste(segment_paste,size, sep = " "), file = "commands", append = TRUE) 
}

system("tac commands > rev_commands")
system("./parallel_launch.sh rev_commands 2")