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comparison PLIDflow/scripts/envelopesmaker.R @ 6:795e11fac81b draft default tip

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Included new tools for standardization
author bitlab
date Wed, 22 Apr 2020 06:12:00 -0400
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5:97f12f7cc852 6:795e11fac81b
1 #envelopesmaker.R makes FILL_Xout.pdb files where X represents values for envelopes 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 envelopesmaker.R <receptor_pdbqt> <session_dir> <pathAutoligand>")
8 }
9
10 #Arguments definition
11 receptor_name <- args[1]
12 session_dir <- args[2]
13 pathLigand <- args[3]
14
15 #recopy <- paste("/home/galaxy/galaxy/tools/proteindocking/scripts/", basename(args[1]), ".txt", sep="")
16 #command <- paste("cp ", args[1], " ", recopy, sep="") #18jun2018
17 #system(command) #18jun2018
18
19 #
20
21 recopy_2 <- scan(paste(basename(args[1]), ".txt", sep=""), what = character(), quiet = TRUE)
22
23
24 #print(paste("es lo que va a salir",recopy_2[1]))
25
26 #Ejecute from R a python script for Running Autoligand
27 sizes_file <- scan("templateenvelopsizes.txt", what = character(), quiet = TRUE)
28
29 path_cajonDesastre <- recopy_2[1]
30
31 segment_paste <- paste("python", pathLigand, "-r", path_cajonDesastre, "-p", sep = " ")
32 #segment_paste <- paste("python /home/eugenia/workflowsoftware/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/AutoLigand.py -r", path_cajonDesastre, "-p", sep = " ")
33
34 #print(segment_paste)
35
36 #print(paste("es lo que va a salir",recopy_2[1]))
37
38 for(i in 1:length(sizes_file)){
39 size <- sizes_file[i]
40
41 ##porcentaje <- (i/length(sizes_file))*100
42
43 ##print(paste(paste(porcentaje, "%", sep = ""),"completed", sep = " "))
44
45
46 # HEMOS TACHADO ESTE SYSTEM
47 print(paste(segment_paste,size, sep = " "))
48
49 # ENABLE THIS SYSTEM
50 #system(paste(segment_paste,size, sep = " "), intern = TRUE)
51 write(paste(segment_paste,size, sep = " "), file = "commands", append = TRUE)
52 }
53
54 system("tac commands > rev_commands")
55 system("./parallel_launch.sh rev_commands 10")
56
57