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comparison PLIDflow/launch_confmaker_multiple.sh @ 0:6fcfa4756040 draft

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author bitlab
date Tue, 14 Jan 2020 06:09:42 -0500
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children b9e7ec4e3cde
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-1:000000000000 0:6fcfa4756040
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