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1 #cluster_to_vina_clusters.R introduces the x, y,z, coordenates of the cluster/-s identified in the vina file configuration how many cluster/-s identified
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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) < 8){
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7 stop("USE: Rscript cluster_to_vina_clusters.R <receptor_name> <ligand_name> <out_PDBQT> <log_file> <eboxsizedata> <session_dir> <receptor_filename> <ligand_filename>")
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8 #stop("USE: Rscript cluster_to_vina_clusters.R <receptor_name> <ligand_name> <out_PDBQT> <log_file> <eboxsizedata> <out_conf_file>")
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9 }
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10
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11 #Arguments definition
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12 receptor_name <- args[1]
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13 ligand_name <- args[2]
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14 out_PDBQT <- args[3]
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15 log_file <- args[4]
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16 eboxsizedata <- args[5]
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17 session_dir <- args[6]
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18 #out_conf_file <- args[6]
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19 receptor_filename <- args[7]
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20 ligand_filename <- args[8]
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21
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22 setwd(session_dir)
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23
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24 #print("before reading table")
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25 clusters_file <- read.table("clusterscoordenates.txt", header = TRUE)
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26 #print("After reading table")
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27
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28 value <- 0
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29 el_b_que_me_quedo <- 1
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30 for(v in 1: nrow(clusters_file)){
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31 coo_x <- clusters_file[v,2]
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32 coo_y <- clusters_file[v,3]
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33 coo_z <- clusters_file[v,4]
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34
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35
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36 #<receptor_PDBQT> <ligand_PDBQT> <out_PDBQT> <log_file> <coo_x > <coo_y> <coo_z> <eboxsizedata> <galaxy out> <v>
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37 argumentos <- paste(args[1],args[2], args[3], args[4], coo_x, coo_y, coo_z, args[5], v, session_dir, sep = " ")
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38 script_argumentos <- paste("Rscript vinafilemarkerclusters.R", argumentos, sep = " ")
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39
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40 system (script_argumentos)
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41 system (paste("vina --config ", paste(v, "_vinaconfig", sep = ""), sep =""))
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42 #system (paste("/home/eugenia/workflowsoftware/autodock_vina_1_1_2_linux_x86/bin/vina --config ", paste(v, "_vinaconfig", sep = ""), sep =""))
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43 #write(paste("/home/eugenia/workflowsoftware/autodock_vina_1_1_2_linux_x86/bin/vina --config ", paste(v, "_vinaconfig", sep = ""), sep =""), file = "commands", append = TRUE)
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44 #
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45
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46 #Save out pdbqt from Vina 30julio2018
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47 #print("before scanning")
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48 outlog_vina <- scan (paste(v, "_vinaconfig", sep = ""), what = character(), quiet = TRUE)
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49 #print("after scanning")
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50
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51 pegar_mv_out9 <- paste("mv", outlog_vina[9], sep = " ")
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52 pegar_v_out <- paste(v,"_", receptor_filename, "_", ligand_filename, "_out_vina.pdbqt", sep = "")
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53 pegar_dos_outs <- paste(pegar_mv_out9, pegar_v_out, sep = " ")
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54
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55
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56 #print(pegar_dos_outs)
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57 system(pegar_dos_outs)
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58
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59 #Save log pdbqt from Vina 30julio2018
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60 pegar_mv_out12 <- paste("mv", outlog_vina[12], sep = " ")
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61 pegar_v_log <- paste(v,"_", receptor_filename, "_", ligand_filename, "_log_vina.log", sep = "")
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62 pegar_dos_logs <- paste(pegar_mv_out12, pegar_v_log, sep = " ")
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63
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64 system(pegar_dos_logs)
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65
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66 #
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67
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68 #binding_mode1_energy <- scan(args[4], what = character(), quiet = TRUE)[122]
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69 #if(v == 1) value <- binding_mode1_energy
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70 #if(value > as.numeric(binding_mode1_energy)){
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71 # value <- as.numeric(binding_mode1_energy)
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72 # el_b_que_me_quedo <- v
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73 #}
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74 }
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75
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76 #copiador <- paste(el_b_que_me_quedo, "_vinaconfig", sep="")
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77 #argumentos <- paste("mv", copiador, out_conf_file, sep=" ")
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78 #print(argumentos)
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79 #system(argumentos)
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80
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81 #system(paste("zip all-vinas-out.zip", "*_out_vina", sep = " ")) #antes del 31julio
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82 #system(paste("mv", "all-vinas-out.zip", args[3] , sep = " ")) #antes del 31julio
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83
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84 #system(paste("zip all-vinas-log.zip", "*_log_vina", sep = " ")) #antes del 31julio
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85 #system(paste("mv", "all-vinas-log.zip", args[4] , sep = " ")) #antes del 31julio
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86
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87 #31julio2018 ----> creo que hay que cambiar los guiones porque hoy se ha quedado pillado en los zip que no lo ha hecho
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88 #30agosto2018 -----> voy a hacer el cambio
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89
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90 # USE THIS FOR keeping stdout but removing stderr
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91 # { cmd 2>&1 >&3 3>&- | logger 3>&-; } 3>&1
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92
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93 system(paste("zip all_vinas_out.zip", "*_out_vina.pdbqt", sep = " ")) #30agosto
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94 system(paste("mv", "all_vinas_out.zip", args[3] , sep = " ")) #30agosto
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95
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96 system(paste("zip all_vinas_log.zip", "*_log_vina.log", sep = " ")) #30agosto
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97 system(paste("mv", "all_vinas_log.zip", args[4] , sep = " ")) #30agosto
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98
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99
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100
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