--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PLIDflow/scripts/cluster_to_vina_cluster.R	Tue Jan 14 06:09:42 2020 -0500
@@ -0,0 +1,100 @@
+#cluster_to_vina_clusters.R introduces the x, y,z, coordenates of the cluster/-s identified in the vina file configuration how many cluster/-s identified 
+
+#!/usr/bin/env Rscript      
+args = commandArgs(trailingOnly=TRUE)
+
+if(length(args) < 8){
+  stop("USE: Rscript cluster_to_vina_clusters.R <receptor_name> <ligand_name> <out_PDBQT> <log_file> <eboxsizedata> <session_dir> <receptor_filename> <ligand_filename>")
+  #stop("USE: Rscript cluster_to_vina_clusters.R <receptor_name> <ligand_name> <out_PDBQT> <log_file> <eboxsizedata> <out_conf_file>")
+}
+
+#Arguments definition 
+receptor_name <- args[1]
+ligand_name <- args[2]
+out_PDBQT <- args[3]
+log_file <- args[4]
+eboxsizedata <- args[5]
+session_dir <- args[6]
+#out_conf_file <- args[6]
+receptor_filename <- args[7]
+ligand_filename <- args[8]
+
+setwd(session_dir)
+
+#print("before reading table")
+clusters_file <- read.table("clusterscoordenates.txt", header = TRUE)
+#print("After reading table")
+
+value <- 0
+el_b_que_me_quedo <- 1
+for(v in 1: nrow(clusters_file)){
+        coo_x <- clusters_file[v,2]
+        coo_y <- clusters_file[v,3]
+        coo_z <- clusters_file[v,4]
+
+
+        #<receptor_PDBQT> <ligand_PDBQT> <out_PDBQT> <log_file> <coo_x > <coo_y> <coo_z> <eboxsizedata> <galaxy out> <v>
+        argumentos <- paste(args[1],args[2], args[3], args[4], coo_x, coo_y, coo_z, args[5], v, session_dir, sep = " ")
+        script_argumentos <- paste("Rscript vinafilemarkerclusters.R", argumentos, sep = " ")
+
+        system (script_argumentos)
+        system (paste("vina --config ", paste(v, "_vinaconfig", sep = ""), sep =""))
+        #system (paste("/home/eugenia/workflowsoftware/autodock_vina_1_1_2_linux_x86/bin/vina --config ", paste(v, "_vinaconfig", sep = ""), sep =""))
+        #write(paste("/home/eugenia/workflowsoftware/autodock_vina_1_1_2_linux_x86/bin/vina --config ", paste(v, "_vinaconfig", sep = ""), sep =""), file = "commands", append = TRUE)
+        #
+        
+	#Save out pdbqt from Vina 30julio2018
+	#print("before scanning")
+	outlog_vina <- scan (paste(v, "_vinaconfig", sep = ""), what = character(), quiet = TRUE)
+	#print("after scanning")
+
+	pegar_mv_out9 <- paste("mv", outlog_vina[9], sep = " ")
+	pegar_v_out <- paste(v,"_", receptor_filename, "_", ligand_filename, "_out_vina.pdbqt", sep = "")
+	pegar_dos_outs <- paste(pegar_mv_out9, pegar_v_out, sep = " ")
+
+	
+	#print(pegar_dos_outs)
+	system(pegar_dos_outs) 
+
+	#Save log pdbqt from Vina 30julio2018
+	pegar_mv_out12 <- paste("mv", outlog_vina[12], sep = " ")
+	pegar_v_log <- paste(v,"_", receptor_filename, "_", ligand_filename, "_log_vina.log", sep = "")
+	pegar_dos_logs <- paste(pegar_mv_out12, pegar_v_log, sep = " ")
+
+	system(pegar_dos_logs) 
+	
+	#
+
+        #binding_mode1_energy <- scan(args[4], what = character(), quiet = TRUE)[122]
+        #if(v == 1) value <- binding_mode1_energy
+        #if(value > as.numeric(binding_mode1_energy)){
+        #        value <- as.numeric(binding_mode1_energy)
+        #        el_b_que_me_quedo <- v
+        #}
+}
+
+#copiador <- paste(el_b_que_me_quedo, "_vinaconfig", sep="")
+#argumentos <- paste("mv", copiador, out_conf_file, sep=" ")
+#print(argumentos)
+#system(argumentos)
+
+#system(paste("zip all-vinas-out.zip", "*_out_vina", sep = " ")) #antes del 31julio
+#system(paste("mv", "all-vinas-out.zip", args[3] , sep = " ")) #antes del 31julio
+
+#system(paste("zip all-vinas-log.zip", "*_log_vina", sep = " ")) #antes del 31julio
+#system(paste("mv", "all-vinas-log.zip", args[4] , sep = " ")) #antes del 31julio
+
+#31julio2018 ----> creo que hay que cambiar los guiones porque hoy se ha quedado pillado en los zip que no lo ha hecho
+#30agosto2018 -----> voy a hacer el cambio 
+
+# USE THIS FOR keeping stdout but removing stderr
+# { cmd 2>&1 >&3 3>&- | logger 3>&-; } 3>&1
+
+system(paste("zip all_vinas_out.zip", "*_out_vina.pdbqt", sep = " ")) #30agosto
+system(paste("mv", "all_vinas_out.zip", args[3] , sep = " ")) #30agosto
+
+system(paste("zip all_vinas_log.zip", "*_log_vina.log", sep = " ")) #30agosto
+system(paste("mv", "all_vinas_log.zip", args[4] , sep = " ")) #30agosto 
+
+
+