|
0
|
1 #clusterfilemaker.R makes a file containg geometric center coordenates for FILL_Xout1.pdb files. X represents envelopes size from 10 to 100
|
|
|
2
|
|
|
3 #!/usr/bin/env Rscript
|
|
|
4 args = commandArgs(trailingOnly=TRUE)
|
|
|
5
|
|
|
6 if(length(args) < 1){
|
|
|
7 stop("USE: Rscript clusterfilemaker.R <session_id>")
|
|
|
8 }
|
|
|
9
|
|
|
10 #Select the directory where all files are being stored
|
|
|
11
|
|
|
12 session_id <- args[1]
|
|
|
13
|
|
|
14 print(session_id)
|
|
|
15
|
|
|
16 setwd(session_id)
|
|
|
17
|
|
|
18 #Scan dataset containig FILL_<point>out1.pdb with point from 10 to 500
|
|
|
19 fill_outs_1 <- scan("templatefillouts1.txt", what = character(), quiet = TRUE)
|
|
|
20
|
|
|
21 #Write the head for the file later created which contains the middle point from FILL_<point>out1.pdb with point from 10 to 500
|
|
|
22 cabecera_fillfile <- paste("npts", sep = ";")
|
|
|
23 cabecera <- c("x","y","z")
|
|
|
24
|
|
|
25 for(i in 1:3){
|
|
|
26 cabecera_fillfile <- paste(cabecera_fillfile, cabecera[i], sep=";")
|
|
|
27 }
|
|
|
28 write(cabecera_fillfile, file="fillouts1file.txt", append= TRUE)
|
|
|
29
|
|
|
30 #Loop to read the files FILL_<point>out1.pdb and calculate the middle point
|
|
|
31 num_points <- 0
|
|
|
32 start_env <- 10 # to fit the first envelope size. In case to change envelope size, only modify this parameter
|
|
|
33 jp <- 10 #jump between envelopes size. In case modify jump between envelopes size, only modify this parameter
|
|
|
34 #In case modify start envelope size and jump, only modify start_env and jp parameters in the script nothing in following steps
|
|
|
35
|
|
|
36
|
|
|
37
|
|
|
38
|
|
|
39
|
|
|
40 num_points <- (start_env - jp)
|
|
|
41 for(f in 1:length(fill_outs_1)){
|
|
|
42 # print(paste("Testing file ", fill_outs_1[f]))
|
|
|
43 if(file_test("-f", fill_outs_1[f])){
|
|
|
44 archivo <- scan(fill_outs_1[f], what = character(), quiet = TRUE)
|
|
|
45 }else{
|
|
|
46 next
|
|
|
47 }
|
|
|
48
|
|
|
49 #Make a table with only x, y, z coordenates for C atoms only
|
|
|
50 salto <- 0
|
|
|
51 for(i in 1:(length(archivo)-2)){
|
|
|
52 if(archivo[i] == "ATOM" && ( archivo[i+2] == "C" || archivo[i+2] == "O" || archivo[i+2] == "H" )){
|
|
|
53 salto <- salto + 1
|
|
|
54 }
|
|
|
55 }
|
|
|
56 tablaC <- matrix(1, nrow = salto, ncol = 4)
|
|
|
57
|
|
|
58 #Names for columns
|
|
|
59 ##First column correspond to position for atoms C. This column will be created when the C atom positions will be know
|
|
|
60 ###Write the name for columns and rows
|
|
|
61 colnames(tablaC) <- c("C Position","X", "Y", "z")
|
|
|
62 rownames(tablaC) <- 1:salto
|
|
|
63
|
|
|
64 #Calculate the number of C atoms and to write theirs coordenates x,y,z in the tablaC
|
|
|
65 salto <- 0
|
|
|
66 posicionC <- c()
|
|
|
67 for(i in 1:(length(archivo)-2)){
|
|
|
68 if(archivo[i] == "ATOM" && ( archivo[i+2] == "C" || archivo[i+2] == "O" || archivo[i+2] == "H" )){
|
|
|
69 salto <- salto + 1
|
|
|
70 posicionC <- c(posicionC, archivo[i+1])
|
|
|
71 tablaC[salto,2] <- as.numeric(archivo[i+5])
|
|
|
72 tablaC[salto,3] <- as.numeric(archivo[i+6])
|
|
|
73 tablaC[salto,4] <- as.numeric(archivo[i+7])
|
|
|
74 }
|
|
|
75 }
|
|
|
76
|
|
|
77 #Write the C atoms positions in column 1 of the table tablaC
|
|
|
78 for(i in 1:salto){
|
|
|
79 tablaC[i,1] <- as.numeric(posicionC[i])
|
|
|
80 }
|
|
|
81
|
|
|
82 #Calculate middle point for the FILL_<point>out1.pdb given
|
|
|
83 pto_x_medio <- (max(tablaC[,2]) + min(tablaC[,2]))/2
|
|
|
84 pto_y_medio <- (max(tablaC[,3]) + min(tablaC[,3]))/2
|
|
|
85 pto_z_medio <- (max(tablaC[,4]) + min(tablaC[,4]))/2
|
|
|
86
|
|
|
87 #Write a plain text called fillouts1file.txt which contain in the first column number of point
|
|
|
88 #for the envelope according to AutoLigand program. Columns 2,3,4 for coordenates x, y ,z
|
|
|
89 #for the middle points for FILL_<point>out1.pdb from 10 to 500 points
|
|
|
90 num_points <- num_points + jp
|
|
|
91 write(paste(num_points,pto_x_medio, pto_y_medio, pto_z_medio, sep=";"),file="fillouts1file.txt", append= TRUE)
|
|
|
92 }
|
|
|
93
|
|
|
94
|
|
|
95
|
|
|
96
|
|
|
97
|
|
|
98
|
|
|
99
|
|
|
100
|
|
|
101
|
