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1 #pdbqtcorrector.R corrests the out PDBQT file from AutoDockTools prepare receptor
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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 pdbqtcorrector.R <receptor_name> <receptor_pdbqt_modified>")
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8 }
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9
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10 #Argument definition
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11 receptor_name <- args[1]
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12
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13 #Scan file
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14 original_file <- scan(args[1], what = character(), quiet = TRUE, na.strings = "NULLAJSKAJSFL")
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15
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16 #Calculate first root word and "TER"
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17 for(e in 1:length(original_file)){
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18 if(original_file[e] == "ATOM" || original_file[e] == "HETATM" || original_file[e] == "TER"){
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19 k <- e
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20 break
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21 }
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22 }
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23
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24 #Calculate the row number for table which conteins aligned x,y,z coordenates
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25 counter <- 0
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26 for(c in e:length(original_file)){
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27 if(original_file[c] == "ATOM" || original_file[c] == "HETATM" || original_file[c] == "TER"){
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28 counter <- counter + 1
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29 }
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30 }
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31
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32 #Table to be fills in named tabla_ordenados
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33 tabla_ordenados <- matrix(1, nrow = (counter), ncol = 13)
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34
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35 #Calculate TER times and make a vector
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36 ele_ter_vector <- 1
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37 ter_vector <- c()
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38 k_position <- c()
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39 for(o in 1:(length(original_file))){
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40 if(original_file[o] =="TER"){
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41 k_position <- c(k_position, o)
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42 for(g in o:(o+4)){
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43 ter_vector <- c(ter_vector,original_file[g] )
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44 }
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45
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46 }
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47 }
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48
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49 #Fill in the tabla_ordenados with values scaned until counter-1 since last row (ter) has diferent length and this could give you back an error
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50 for(i in 1:(counter-1)){
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51 for(j in 1:13){
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52 tabla_ordenados[i,j] <- original_file[k]
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53 if(tabla_ordenados[i,13]=="ATOM" || tabla_ordenados[i,13]== "HETATM"|| tabla_ordenados[i,13]=="TER"){
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54 corte <- c()
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55 for(v in 4:12){
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56 corte <- c(corte,tabla_ordenados[i,v])
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57 }
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58 coo_corte <- 1
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59 tabla_ordenados[i,4] <- ""
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60 for(m in 5:13){
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61 tabla_ordenados[i,m] <- corte[coo_corte]
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62 coo_corte <- coo_corte + 1
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63 }
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64 k <- k-1
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65 }
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66 k <- k + 1
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67 }
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68 if(tabla_ordenados[i,1]=="TER"){
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69 k <- k - 8
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70 }
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71 }
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72
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73
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74 #Fill in TER row until last one
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75 star_ter <- 2
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76 mmm <- 1
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77 for(ii in 1:counter){
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78 if(tabla_ordenados[ii,1]=="TER"){
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79 k <- k_position[mmm] + 4
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80 mmm <- mmm + 1
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81 y <- 2
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82 for(l in star_ter:(star_ter+3)){
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83 if(y%%3==0 && y!=6){
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84 tabla_ordenados[ii,y] <- ""
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85 y <- y + 1
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86 tabla_ordenados[ii,y] <- ter_vector[l]
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87 }
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88 tabla_ordenados[ii,y] <- ter_vector[l]
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89 y <- y +1
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90 }
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91 star_ter <- star_ter + 5
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92 for(b in 7:13){
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93 tabla_ordenados[ii,b] <- ""
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94 }
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95 }
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96 }
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97
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98 #Fill in last row with TER row values
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99 last_ter <- length(ter_vector)-4
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100 for(jj in 1:6){
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101 tabla_ordenados[counter,jj] <- ter_vector[last_ter]
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102 if(jj%%3==0 && jj !=6){
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103 tabla_ordenados[counter, jj] <- ""
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104 last_ter <- last_ter - 1
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105 }
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106 last_ter <- last_ter + 1
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107 }
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108 for(jj in 7:13){
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109 tabla_ordenados[counter, jj] <- ""
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110 }
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111
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112 #View(tabla_ordenados)
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113
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114 #Write oredered table in a PDBQT file
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115 for(xi in 1:nrow(tabla_ordenados)){
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116 cabecera <- tabla_ordenados[xi,1]
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117 for(xj in 2:13){
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118 cabecera <- paste(cabecera, tabla_ordenados[xi,xj], sep = " ")
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119 }
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120 write(cabecera, file = args[2], append = TRUE)
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121 }
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