--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PLIDflow/scripts/pdbqtcorrector.R	Tue Jan 14 07:52:48 2020 -0500
@@ -0,0 +1,128 @@
+#pdbqtcorrector.R corrests the out PDBQT file from AutoDockTools prepare receptor 
+
+#!/usr/bin/env Rscript      
+args = commandArgs(trailingOnly=TRUE) 
+
+if(length(args) < 1){
+  stop("USE: Rscript pdbqtcorrector.R <receptor_name> <receptor_pdbqt_modified>")
+}
+
+#Argument definition
+receptor_name <- args[1]
+
+#Scan file
+original_file <- scan(args[1], what = character(), quiet = TRUE, na.strings = "NULLAJSKAJSFL")
+
+#Calculate first root word and "TER"
+for(e in 1:length(original_file)){
+  if(original_file[e] == "ATOM" || original_file[e] == "HETATM" || original_file[e] == "TER"){
+    k <- e
+    break
+  }
+}
+
+#Calculate the row number for table which conteins aligned x,y,z coordenates 
+counter <- 0
+for(c in e:length(original_file)){
+  if(original_file[c] == "ATOM" || original_file[c] == "HETATM" || original_file[c] == "TER"){
+    counter <- counter + 1
+  }
+}
+
+#Table to be fills in named tabla_ordenados
+tabla_ordenados <- matrix(1, nrow = (counter), ncol = 13)
+
+#Calculate TER times and make a vector
+ele_ter_vector <- 1
+ter_vector <- c()
+k_position <- c()
+for(o in 1:(length(original_file))){
+  if(original_file[o] =="TER"){
+    k_position <- c(k_position, o)
+    for(g in o:(o+4)){
+      ter_vector <- c(ter_vector,original_file[g] )
+    }
+    
+  }
+}
+
+#Fill in the tabla_ordenados with values scaned until counter-1 since last row (ter) has diferent length and this could give you back an error
+for(i in 1:(counter-1)){
+  for(j in 1:13){
+    tabla_ordenados[i,j] <- original_file[k]
+    if(tabla_ordenados[i,13]=="ATOM" || tabla_ordenados[i,13]== "HETATM"|| tabla_ordenados[i,13]=="TER"){
+      corte <- c()
+      for(v in 4:12){
+        corte <- c(corte,tabla_ordenados[i,v])
+      }
+      coo_corte <- 1
+      tabla_ordenados[i,4] <- ""
+      for(m in 5:13){
+        tabla_ordenados[i,m] <- corte[coo_corte]
+        coo_corte <- coo_corte + 1
+      }
+      k <- k-1
+    }
+    k <- k + 1 
+  }
+  if(tabla_ordenados[i,1]=="TER"){
+    k <- k - 8
+  } 
+}
+
+
+#Fill in TER row until last one 
+star_ter <- 2
+mmm <- 1
+for(ii in 1:counter){
+  if(tabla_ordenados[ii,1]=="TER"){
+    k <- k_position[mmm] + 4
+    mmm <- mmm + 1
+    y <- 2
+    for(l in star_ter:(star_ter+3)){
+      if(y%%3==0 && y!=6){
+        tabla_ordenados[ii,y] <- ""
+        y <- y + 1
+        tabla_ordenados[ii,y] <- ter_vector[l]
+      }
+      tabla_ordenados[ii,y] <- ter_vector[l]
+      y <- y +1
+    }
+    star_ter <- star_ter + 5
+    for(b in 7:13){
+      tabla_ordenados[ii,b] <- ""
+    }
+  }
+}
+
+#Fill in last row with TER row values 
+last_ter <- length(ter_vector)-4
+for(jj in 1:6){
+  tabla_ordenados[counter,jj] <- ter_vector[last_ter]
+  if(jj%%3==0 && jj !=6){
+    tabla_ordenados[counter, jj] <- ""
+    last_ter <- last_ter - 1
+  }
+  last_ter <- last_ter + 1
+}
+for(jj in 7:13){
+  tabla_ordenados[counter, jj] <- ""
+}
+
+#View(tabla_ordenados)
+
+#Write oredered table in a PDBQT file
+for(xi in 1:nrow(tabla_ordenados)){
+  cabecera <- tabla_ordenados[xi,1]
+  for(xj in 2:13){
+    cabecera <- paste(cabecera, tabla_ordenados[xi,xj], sep = " ")
+  }
+  write(cabecera, file = args[2], append = TRUE)
+}
+
+
+
+
+
+
+