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