--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PLIDflow/launch_confmaker_multiple.sh	Tue Jan 14 06:09:42 2020 -0500
@@ -0,0 +1,76 @@
+receptor_pdbqt=$1
+receptor_pdbqt_modified=$2
+receptor_pdbqt_modified2=$3
+ligand_pdbqt=$4
+size_x=$5
+out=$6
+log=$7
+receptor_name=$8
+ligand_name=$9
+# This one is to extract the protein code and to check whether the fillouts have already been done
+# This is for the parallel version, ignore
+receptor_file=${10}
+receptorTypes=${11}
+toolsDirectory=${12}
+
+# Configuration variables // This is not really necessary anymore
+MYRAND=$(( ( RANDOM % 10000000 )  + 1 ))
+RANDDIR=${MYRAND}
+
+
+
+
+
+mkdir $RANDDIR
+
+
+cp -r ${toolsDirectory}/scripts/* $RANDDIR
+echo "$toolsDirectory"
+
+cp $receptorTypes $RANDDIR
+NOMBRERECEPTOR=$(basename $receptorTypes)
+mv $RANDDIR/$NOMBRERECEPTOR $RANDDIR/receptor_atm_types.txt
+
+MYPWD=$PWD
+
+
+cd $RANDDIR
+
+source ADT_VENV/bin/activate
+
+#echo "[RUNNING] - (Rscript pdbcenter_npts_finder.R $receptor_pdbqt_modified $RANDDIR) &>/dev/null"
+Rscript pdbcenter_npts_finder.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR
+
+#echo "[RUNNING] - (Rscript gpffilemaker.R $receptor_pdbqt $RANDDIR) "
+Rscript gpffilemaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR
+
+#echo "[RUNNING] - (Rscript glgfilemaker.R $receptor_pdbqt $RANDDIR) "
+Rscript glgfilemaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR
+
+#echo "[RUNNING] - (Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) "
+#(Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) &>/dev/null
+pathLigand=$(which AutoLigand.py)
+Rscript envelopesmaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR $pathLigand
+
+#cp ~/proteindb/2E9U_PH7/FILL* .
+
+#echo "[RUNNING] - (Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) "
+#(Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) &>/dev/null
+
+
+#echo "[RUNNING] - (Rscript clusterfilemaker.R $RANDDIR) "
+Rscript clusterfilemaker.R $MYPWD/$RANDDIR
+
+
+#echo "[RUNNING] - (Rscript clusterfinder_Auto.R $RANDDIR) "
+Rscript clusterfinder_Auto.R $MYPWD/$RANDDIR
+
+
+#echo "[RUNNING] - (Rscript cluster_to_vina_cluster.R $receptor_pdbqt_modified2 $ligand_pdbqt $out $log $size_x $RANDDIR $receptor_name $ligand_name) "
+Rscript cluster_to_vina_cluster.R $receptor_pdbqt_modified2 $ligand_pdbqt $out $log $size_x $MYPWD/$RANDDIR $receptor_name $ligand_name
+
+
+cd $MYPWD
+
+
+deactivate