--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PLIDflow/scripts/envelopesmaker.R	Tue Jan 14 06:09:42 2020 -0500
@@ -0,0 +1,57 @@
+#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")
+
+