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0
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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=$9
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10 # This one is to extract the protein code and to check whether the fillouts have already been done
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11 # This is for the parallel version, ignore
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12 receptor_file=${10}
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13 receptorTypes=${11}
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14 toolsDirectory=${12}
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15
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16 # Configuration variables // This is not really necessary anymore
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17 MYRAND=$(( ( RANDOM % 10000000 ) + 1 ))
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18 RANDDIR=${MYRAND}
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19
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20
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21
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22
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23
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24 mkdir $RANDDIR
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25
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26
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27 cp -r ${toolsDirectory}/scripts/* $RANDDIR
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28 echo "$toolsDirectory"
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29
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30 cp $receptorTypes $RANDDIR
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31 NOMBRERECEPTOR=$(basename $receptorTypes)
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32 mv $RANDDIR/$NOMBRERECEPTOR $RANDDIR/receptor_atm_types.txt
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33
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34 MYPWD=$PWD
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35
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36
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37 cd $RANDDIR
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38
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39 source ADT_VENV/bin/activate
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40
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41 #echo "[RUNNING] - (Rscript pdbcenter_npts_finder.R $receptor_pdbqt_modified $RANDDIR) &>/dev/null"
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4
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42 (Rscript pdbcenter_npts_finder.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR) 2>&1
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0
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43
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44 #echo "[RUNNING] - (Rscript gpffilemaker.R $receptor_pdbqt $RANDDIR) "
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4
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45 (Rscript gpffilemaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR) 2>&1
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0
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46
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47 #echo "[RUNNING] - (Rscript glgfilemaker.R $receptor_pdbqt $RANDDIR) "
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4
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48 (Rscript glgfilemaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR) 2>&1
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0
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49
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50 #echo "[RUNNING] - (Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) "
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51 #(Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) &>/dev/null
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52 pathLigand=$(which AutoLigand.py)
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4
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53 (Rscript envelopesmaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR $pathLigand) 2>&1
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0
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54
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55 #cp ~/proteindb/2E9U_PH7/FILL* .
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56
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57 #echo "[RUNNING] - (Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) "
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58 #(Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) &>/dev/null
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59
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60
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61 #echo "[RUNNING] - (Rscript clusterfilemaker.R $RANDDIR) "
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4
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62 (Rscript clusterfilemaker.R $MYPWD/$RANDDIR) 2>&1
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0
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63
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64
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65 #echo "[RUNNING] - (Rscript clusterfinder_Auto.R $RANDDIR) "
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4
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66 (Rscript clusterfinder_Auto.R $MYPWD/$RANDDIR) 2>&1
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0
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67
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68
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69 #echo "[RUNNING] - (Rscript cluster_to_vina_cluster.R $receptor_pdbqt_modified2 $ligand_pdbqt $out $log $size_x $RANDDIR $receptor_name $ligand_name) "
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4
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70 (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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0
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71
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72
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73 cd $MYPWD
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74
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75
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76 deactivate
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