|
0
|
1 #gpffilemaker makes the GPF file
|
|
|
2
|
|
|
3 #!/usr/bin/env Rscript
|
|
|
4 args = commandArgs(trailingOnly=TRUE)
|
|
|
5
|
|
|
6 if(length(args) < 1){
|
|
|
7 stop("USE: Rscript gpffilemaker.R <receptor_name> <session_dir>")
|
|
|
8 }
|
|
|
9
|
|
|
10 #Read file containing PDB geometric center and number of points x, y ,z
|
|
|
11 #archivo_center_npts <- scan("/home/galaxy/galaxy/tools/proteindocking/scripts/pdbcenter_npts.txt", what = character(), quiet = TRUE)
|
|
|
12 archivo_center_npts <- scan("pdbcenter_npts.txt", what = character(), quiet = TRUE)
|
|
|
13
|
|
|
14 #Read file containing receptor atom types
|
|
|
15 ver <- scan("receptor_atm_types.txt", what = character(), quiet = TRUE, na.strings = "NULLAJSKAJSFL")
|
|
|
16
|
|
|
17
|
|
|
18 #Arguments definition
|
|
|
19 receptor_name <- args[1]
|
|
|
20 session_dir <- args[2]
|
|
|
21 aux_receptor_name <- basename(args[1])
|
|
|
22 #aux_receptor_name <- paste("/home/galaxy/galaxy/tools/proteindocking/scripts/", basename(args[1]), sep="")
|
|
|
23 npts_x <- archivo_center_npts[4]
|
|
|
24 npts_y <- archivo_center_npts[5]
|
|
|
25 npts_z <- archivo_center_npts[6]
|
|
|
26 gridcenter_x <- archivo_center_npts[1]
|
|
|
27 gridcenter_y <- archivo_center_npts[2]
|
|
|
28 gridcenter_z <- archivo_center_npts[3]
|
|
|
29
|
|
|
30 #Creation of the GPF file
|
|
|
31 #Row 1
|
|
|
32 fila_1_e1 <- paste("npts", npts_x, sep = " ")
|
|
|
33 fila_1_e2 <- paste(fila_1_e1, npts_y, sep = " ")
|
|
|
34 fila_1_e3 <- paste(fila_1_e2, npts_z, sep = " ")
|
|
|
35 fila_1 <- paste(fila_1_e3, "# num.grid points in xyz", sep = " ")
|
|
|
36
|
|
|
37 #Row 2
|
|
|
38 fila_2_e2 <- paste(aux_receptor_name, ".maps.fld", sep = "")
|
|
|
39 fila_2_e1 <- paste("gridfld", fila_2_e2, sep = " " )
|
|
|
40 fila_2 <- paste(fila_2_e1, "# grid_data_file", sep = " ")
|
|
|
41
|
|
|
42 #Row 3
|
|
|
43 fila_3 <- paste("spacing 1.0", "# spacing(A)", sep = " ")
|
|
|
44
|
|
|
45 #Row 4
|
|
|
46 #fila_4 <- paste("receptor_types A C HD N NA OA S SA", "# receptor atom types", sep = " ")
|
|
|
47 cabecera_f4 <- ver[1]
|
|
|
48 vector_f4 <- c()
|
|
|
49 for(f4 in 2:length(ver)){
|
|
|
50 cabecera_f4 <- paste(cabecera_f4, ver[f4], sep = " ")
|
|
|
51 }
|
|
|
52
|
|
|
53 fila_4 <- paste("receptor_types", cabecera_f4, "# receptor atom types", sep = " ")
|
|
|
54 #print(fila_4)
|
|
|
55
|
|
|
56 #Row 5
|
|
|
57 fila_5 <- paste("ligand_types C HD OA", "# ligand atom types", sep = " ")
|
|
|
58
|
|
|
59 #Row 6
|
|
|
60 fila_6_e2 <- paste(aux_receptor_name, ".pdbqt", sep = "")
|
|
|
61 fila_6_e1 <- paste("receptor", fila_6_e2, sep = " ")
|
|
|
62 fila_6 <- paste(fila_6_e1, "# macromolecule", sep = " ")
|
|
|
63
|
|
|
64 #Row 7
|
|
|
65 fila_7_e1 <- paste("gridcenter",gridcenter_x, sep = " ")
|
|
|
66 fila_7_e2 <- paste(fila_7_e1, gridcenter_y, sep = " ")
|
|
|
67 fila_7_e3 <- paste(fila_7_e2, gridcenter_z, sep = " ")
|
|
|
68 fila_7 <- paste(fila_7_e3, "# xyz-coordinates or auto", sep = " ")
|
|
|
69
|
|
|
70 #Row 8
|
|
|
71 fila_8 <- paste("smooth 0.5", "# store minimum energy w/in rad(A)", sep = " ")
|
|
|
72
|
|
|
73 #Row 9
|
|
|
74 fila_9_e2 <- paste(aux_receptor_name, ".C.map", sep = "")
|
|
|
75 fila_9_e1 <- paste("map", fila_9_e2, sep = " ")
|
|
|
76 fila_9 <- paste(fila_9_e1, "# atom-specific affinity map", sep = " ")
|
|
|
77
|
|
|
78 #Row 10
|
|
|
79 fila_10_e2 <- paste(aux_receptor_name, ".HD.map", sep = "")
|
|
|
80 fila_10_e1 <- paste("map",fila_10_e2, sep = " ")
|
|
|
81 fila_10 <- paste(fila_10_e1, "# atom-specific affinity map", sep = " ")
|
|
|
82
|
|
|
83 #Row 11
|
|
|
84 fila_11_e2 <- paste(aux_receptor_name, ".OA.map", sep = "")
|
|
|
85 fila_11_e1 <- paste("map", fila_11_e2, sep = " ")
|
|
|
86 fila_11 <- paste(fila_11_e1, "# atom-specific affinity map", sep = " ")
|
|
|
87
|
|
|
88 #Row 12
|
|
|
89 fila_12_e2 <- paste(aux_receptor_name, ".e.map", sep = "")
|
|
|
90 fila_12_e1 <- paste("elecmap", fila_12_e2, sep = " ")
|
|
|
91 fila_12 <- paste(fila_12_e1, "# electrostatic potential map", sep = " ")
|
|
|
92
|
|
|
93 #Row 13
|
|
|
94 fila_13_e2 <- paste(aux_receptor_name, ".d.map", sep = "")
|
|
|
95 fila_13_e1 <- paste("dsolvmap", fila_13_e2, sep = " ")
|
|
|
96 fila_13 <- paste(fila_13_e1, "# desolvation potential map", sep = " ")
|
|
|
97
|
|
|
98 #Row 14
|
|
|
99 fila_14 <- paste("dielectric -0.1465", "# <0, AD4 distance-dep.diel;>0, constant", sep = " ")
|
|
|
100
|
|
|
101 #Paste all rows with a line jump for separation
|
|
|
102 filas <- c(fila_1, fila_2, fila_3, fila_4, fila_5, fila_6, fila_7, fila_8, fila_9, fila_10, fila_11, fila_12, fila_13, fila_14)
|
|
|
103
|
|
|
104 datos<- c()
|
|
|
105 for(i in 1:14){
|
|
|
106 datos <- paste(c(datos, filas[i]))
|
|
|
107 }
|
|
|
108
|
|
|
109 #nombre_final <- paste("/home/galaxy/galaxy/tools/proteindocking/scripts/", basename(args[1]), ".gpf", sep="")
|
|
|
110 nombre_final <- paste(basename(args[1]), ".gpf", sep="")
|
|
|
111
|
|
|
112 write(datos, file=nombre_final, append = FALSE)
|
|
|
113
|
|
|
114 #write(basename(args[1]), file= paste("/home/galaxy/galaxy/tools/proteindocking/scripts/", basename(args[1]), ".txt", sep="")) #parte añadida 18jun2018
|
|
|
115 write(basename(args[1]), file= paste(basename(args[1]), ".txt", sep="")) #parte añadida 18jun2018
|
|
|
116
|
