Mercurial > repos > bitlab > plidflow
diff PLIDflow/scripts/envelopesmaker.R @ 6:795e11fac81b draft default tip
Included new tools for standardization
author | bitlab |
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date | Wed, 22 Apr 2020 06:12:00 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/envelopesmaker.R Wed Apr 22 06:12:00 2020 -0400 @@ -0,0 +1,57 @@ +#envelopesmaker.R makes FILL_Xout.pdb files where X represents values for envelopes from 10 to 100 + +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) + +if(length(args) < 1){ + stop("USE: Rscript envelopesmaker.R <receptor_pdbqt> <session_dir> <pathAutoligand>") +} + +#Arguments definition +receptor_name <- args[1] +session_dir <- args[2] +pathLigand <- args[3] + +#recopy <- paste("/home/galaxy/galaxy/tools/proteindocking/scripts/", basename(args[1]), ".txt", sep="") +#command <- paste("cp ", args[1], " ", recopy, sep="") #18jun2018 +#system(command) #18jun2018 + +# + +recopy_2 <- scan(paste(basename(args[1]), ".txt", sep=""), what = character(), quiet = TRUE) + + +#print(paste("es lo que va a salir",recopy_2[1])) + +#Ejecute from R a python script for Running Autoligand +sizes_file <- scan("templateenvelopsizes.txt", what = character(), quiet = TRUE) + +path_cajonDesastre <- recopy_2[1] + +segment_paste <- paste("python", pathLigand, "-r", path_cajonDesastre, "-p", sep = " ") +#segment_paste <- paste("python /home/eugenia/workflowsoftware/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/AutoLigand.py -r", path_cajonDesastre, "-p", sep = " ") + +#print(segment_paste) + +#print(paste("es lo que va a salir",recopy_2[1])) + +for(i in 1:length(sizes_file)){ +size <- sizes_file[i] + +##porcentaje <- (i/length(sizes_file))*100 + +##print(paste(paste(porcentaje, "%", sep = ""),"completed", sep = " ")) + + +# HEMOS TACHADO ESTE SYSTEM +print(paste(segment_paste,size, sep = " ")) + +# ENABLE THIS SYSTEM +#system(paste(segment_paste,size, sep = " "), intern = TRUE) +write(paste(segment_paste,size, sep = " "), file = "commands", append = TRUE) +} + +system("tac commands > rev_commands") +system("./parallel_launch.sh rev_commands 10") + +