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6
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1 receptor_pdbqt=$1
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2 receptor_pdbqt_modified=$2
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3 receptor_pdbqt_modified2=$3
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4 ligand_pdbqt=$4
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5 size_x=$5
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6 out=$6
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7 log=$7
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8 receptor_name=$8
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9 ligand_name=$9
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10 receptor_file=${10}
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11 receptorTypes=${11}
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12 toolsDirectory=${12}
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13
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14 MYRAND=$(( ( RANDOM % 10000000 ) + 1 ))
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15 RANDDIR=${MYRAND}
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16
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17
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18 # ENABLE PROTEIN CODE
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19 proteinCode=$(echo ${13} | awk '{print toupper($0)}')
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20
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21 # ENABLE PROTEIN CODE
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22 #PROTEINDB=${YOUR_PATH_TO_FOLDER_DB}
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23 PROTEINDB=/home/galaxy-bitlab/proteindb
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24
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25
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26
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27 mkdir $RANDDIR
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28
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29
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30 cp -r ${toolsDirectory}/scripts/* $RANDDIR
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31
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32 cp $receptorTypes $RANDDIR
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33 NOMBRERECEPTOR=$(basename $receptorTypes)
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34 mv $RANDDIR/$NOMBRERECEPTOR $RANDDIR/receptor_atm_types.txt
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35
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36 MYPWD=$PWD
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37
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38
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39 cd $RANDDIR
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40
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41 source ADT_VENV/bin/activate
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42
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43 (Rscript pdbcenter_npts_finder.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR) 2>&1
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44
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45 (Rscript gpffilemaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR) 2>&1
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46
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47 (Rscript glgfilemaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR) 2>&1
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48
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49 echo "[INFO] Working path: $PWD"
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50
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51
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52 proteinPath=$PROTEINDB/$proteinCode
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53 echo "[INFO] - Extracting protein code [$proteinPath]"
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54 isRandomID="FALSE"
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55 if [ "$proteinCode" == "X__OC__PROTEINCODE__CC__" ]
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56 then
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57 isRandomID="TRUE"
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58 echo "No protein code supplied"
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59 fi
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60
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61 filloutsNum=0
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62 filloutsAreGood=1
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63 if [ -d "$proteinPath" ] && [ $isRandomID == "FALSE" ]; then
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64
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65 for x in {10..600..10}
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66 do
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67 filloutsNum=$(ls -lh $PROTEINDB/$proteinCode/FILL_${x}out* 2> /dev/null | wc -l)
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68 if [ $filloutsNum -eq 0 ]; then
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69 filloutsAreGood=0
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70 echo "[INFO] Did not find fillout $x"
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71 fi
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72 done
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73 else
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74 filloutsAreGood=0
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75 fi
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76
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77 if [ -d "$proteinPath" ] && [ $filloutsAreGood -eq 1 ] && [ $isRandomID == "FALSE" ]; then
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78 echo "[INFO] Found protein in database. Reusing envelopes."
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79 cp $proteinPath/FILL* .
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80 else
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81 echo "[INFO] Did not find protein in database. Computing envelopes."
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82 pathLigand=$(which AutoLigand.py)
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83 (Rscript envelopesmaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR $pathLigand) 2>&1
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84 mkdir $proteinPath
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85 cp FILL* $proteinPath
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86
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87 fi
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88
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89
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90 (Rscript clusterfilemaker.R $MYPWD/$RANDDIR) 2>&1
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91
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92 (Rscript clusterfinder_Auto.R $MYPWD/$RANDDIR) 2>&1
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93
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94 (Rscript cluster_to_vina_cluster.R $receptor_pdbqt_modified2 $ligand_pdbqt $out $log $size_x $MYPWD/$RANDDIR $receptor_name $ligand_name) 2>&1
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95
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96
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97 rm -rf ./CONDA_RDKIT_ENV
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98 rm -rf ./ADT_VENV
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99
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100 cd $MYPWD
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101
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102
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103 deactivate
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