|
0
|
1 receptor_pdbqt=$1
|
|
|
2 receptor_pdbqt_modified=$2
|
|
|
3 receptor_pdbqt_modified2=$3
|
|
|
4 ligand_pdbqt=$4
|
|
|
5 size_x=$5
|
|
|
6 out=$6
|
|
|
7 log=$7
|
|
|
8 receptor_name=$8
|
|
|
9 ligand_name=$9
|
|
|
10 # This one is to extract the protein code and to check whether the fillouts have already been done
|
|
|
11 # This is for the parallel version, ignore
|
|
|
12 receptor_file=${10}
|
|
|
13 receptorTypes=${11}
|
|
|
14 toolsDirectory=${12}
|
|
|
15
|
|
|
16 # Configuration variables // This is not really necessary anymore
|
|
|
17 MYRAND=$(( ( RANDOM % 10000000 ) + 1 ))
|
|
|
18 RANDDIR=${MYRAND}
|
|
|
19
|
|
|
20
|
|
|
21
|
|
|
22
|
|
|
23
|
|
|
24 mkdir $RANDDIR
|
|
|
25
|
|
|
26
|
|
|
27 cp -r ${toolsDirectory}/scripts/* $RANDDIR
|
|
|
28 echo "$toolsDirectory"
|
|
|
29
|
|
|
30 cp $receptorTypes $RANDDIR
|
|
|
31 NOMBRERECEPTOR=$(basename $receptorTypes)
|
|
|
32 mv $RANDDIR/$NOMBRERECEPTOR $RANDDIR/receptor_atm_types.txt
|
|
|
33
|
|
|
34 MYPWD=$PWD
|
|
|
35
|
|
|
36
|
|
|
37 cd $RANDDIR
|
|
|
38
|
|
|
39 source ADT_VENV/bin/activate
|
|
|
40
|
|
|
41 #echo "[RUNNING] - (Rscript pdbcenter_npts_finder.R $receptor_pdbqt_modified $RANDDIR) &>/dev/null"
|
|
|
42 Rscript pdbcenter_npts_finder.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR
|
|
|
43
|
|
|
44 #echo "[RUNNING] - (Rscript gpffilemaker.R $receptor_pdbqt $RANDDIR) "
|
|
|
45 Rscript gpffilemaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR
|
|
|
46
|
|
|
47 #echo "[RUNNING] - (Rscript glgfilemaker.R $receptor_pdbqt $RANDDIR) "
|
|
|
48 Rscript glgfilemaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR
|
|
|
49
|
|
|
50 #echo "[RUNNING] - (Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) "
|
|
|
51 #(Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) &>/dev/null
|
|
|
52 pathLigand=$(which AutoLigand.py)
|
|
|
53 Rscript envelopesmaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR $pathLigand
|
|
|
54
|
|
|
55 #cp ~/proteindb/2E9U_PH7/FILL* .
|
|
|
56
|
|
|
57 #echo "[RUNNING] - (Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) "
|
|
|
58 #(Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) &>/dev/null
|
|
|
59
|
|
|
60
|
|
|
61 #echo "[RUNNING] - (Rscript clusterfilemaker.R $RANDDIR) "
|
|
|
62 Rscript clusterfilemaker.R $MYPWD/$RANDDIR
|
|
|
63
|
|
|
64
|
|
|
65 #echo "[RUNNING] - (Rscript clusterfinder_Auto.R $RANDDIR) "
|
|
|
66 Rscript clusterfinder_Auto.R $MYPWD/$RANDDIR
|
|
|
67
|
|
|
68
|
|
|
69 #echo "[RUNNING] - (Rscript cluster_to_vina_cluster.R $receptor_pdbqt_modified2 $ligand_pdbqt $out $log $size_x $RANDDIR $receptor_name $ligand_name) "
|
|
|
70 Rscript cluster_to_vina_cluster.R $receptor_pdbqt_modified2 $ligand_pdbqt $out $log $size_x $MYPWD/$RANDDIR $receptor_name $ligand_name
|
|
|
71
|
|
|
72
|
|
|
73 cd $MYPWD
|
|
|
74
|
|
|
75
|
|
|
76 deactivate
|
