--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PLIDflow/scripts/clusterfilemaker.R	Tue Jan 14 06:09:42 2020 -0500
@@ -0,0 +1,101 @@
+#clusterfilemaker.R makes a file containg geometric center coordenates for FILL_Xout1.pdb files. X represents envelopes size from 10 to 100    
+
+#!/usr/bin/env Rscript      
+args = commandArgs(trailingOnly=TRUE) 
+
+if(length(args) < 1){
+  stop("USE: Rscript clusterfilemaker.R <session_id>")
+}
+
+#Select the directory where all files are being stored 
+
+session_id <- args[1]
+
+print(session_id)
+
+setwd(session_id) 
+
+#Scan dataset containig FILL_<point>out1.pdb with point from 10 to 500
+fill_outs_1 <- scan("templatefillouts1.txt", what = character(), quiet = TRUE)
+
+#Write the head for the file later created which contains the middle point from FILL_<point>out1.pdb with point from 10 to 500 
+cabecera_fillfile <- paste("npts", sep = ";")
+cabecera <- c("x","y","z")
+
+for(i in 1:3){
+  cabecera_fillfile <- paste(cabecera_fillfile, cabecera[i], sep=";")
+}
+write(cabecera_fillfile, file="fillouts1file.txt", append= TRUE) 
+
+#Loop to read the files FILL_<point>out1.pdb and calculate the middle point
+num_points <- 0
+start_env <- 10 # to fit the first envelope size. In case to change envelope size, only modify this parameter
+jp <- 10 #jump between envelopes size. In case modify jump between envelopes size, only modify this parameter
+#In case modify start envelope size and jump, only modify start_env and jp parameters in the script nothing in following steps
+
+
+
+
+
+num_points <- (start_env - jp)
+for(f in 1:length(fill_outs_1)){
+#	print(paste("Testing file ", fill_outs_1[f]))
+    if(file_test("-f", fill_outs_1[f])){ 
+      archivo <- scan(fill_outs_1[f], what = character(), quiet = TRUE)
+    }else{
+	    next
+    }
+  
+#Make a table with only x, y, z coordenates for C atoms only
+salto <- 0
+for(i in 1:(length(archivo)-2)){
+ if(archivo[i] == "ATOM" && ( archivo[i+2] == "C" || archivo[i+2] == "O" || archivo[i+2] == "H" )){
+    salto <- salto + 1
+  }
+}
+tablaC <- matrix(1, nrow = salto, ncol = 4)
+
+#Names for columns
+##First column correspond to position for atoms C. This column will be created when the C atom positions will be know
+###Write the name for columns and rows
+colnames(tablaC) <- c("C Position","X", "Y", "z")
+rownames(tablaC) <- 1:salto
+  
+#Calculate the number of C atoms and to write theirs coordenates x,y,z in the tablaC
+salto <- 0
+posicionC <-  c()
+for(i in 1:(length(archivo)-2)){
+ if(archivo[i] == "ATOM" && ( archivo[i+2] == "C" || archivo[i+2] == "O" || archivo[i+2] == "H" )){
+    salto <- salto + 1
+    posicionC <- c(posicionC, archivo[i+1])
+    tablaC[salto,2] <- as.numeric(archivo[i+5])
+    tablaC[salto,3] <- as.numeric(archivo[i+6])
+    tablaC[salto,4] <- as.numeric(archivo[i+7])
+  }
+}
+  
+#Write the C atoms positions in column 1 of the table tablaC
+for(i in 1:salto){
+tablaC[i,1] <- as.numeric(posicionC[i]) 
+}
+  
+#Calculate middle point for the FILL_<point>out1.pdb given
+pto_x_medio <- (max(tablaC[,2]) + min(tablaC[,2]))/2
+pto_y_medio <- (max(tablaC[,3]) + min(tablaC[,3]))/2
+pto_z_medio <- (max(tablaC[,4]) + min(tablaC[,4]))/2
+  
+#Write a plain text called fillouts1file.txt which contain in the first column number of point  
+#for the envelope according to AutoLigand program. Columns 2,3,4 for coordenates x, y ,z 
+#for the middle points for FILL_<point>out1.pdb from 10 to 500 points
+num_points <- num_points + jp
+write(paste(num_points,pto_x_medio, pto_y_medio, pto_z_medio, sep=";"),file="fillouts1file.txt", append= TRUE)
+}
+
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