Mercurial > repos > bitlab > plidflow
comparison PLIDflow/scripts/gpffilemaker.R @ 0:6fcfa4756040 draft
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author | bitlab |
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date | Tue, 14 Jan 2020 06:09:42 -0500 |
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-1:000000000000 | 0:6fcfa4756040 |
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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 |