--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PLIDflow/launch_confmaker_multiple.sh	Wed Apr 22 06:12:00 2020 -0400
@@ -0,0 +1,103 @@
+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=$9
+receptor_file=${10}
+receptorTypes=${11}
+toolsDirectory=${12}
+
+MYRAND=$(( ( RANDOM % 10000000 )  + 1 ))
+RANDDIR=${MYRAND}
+
+
+# ENABLE PROTEIN CODE
+proteinCode=$(echo ${13} | awk '{print toupper($0)}')
+
+# ENABLE PROTEIN CODE
+#PROTEINDB=${YOUR_PATH_TO_FOLDER_DB}
+PROTEINDB=/home/galaxy-bitlab/proteindb
+
+
+
+mkdir $RANDDIR
+
+
+cp -r ${toolsDirectory}/scripts/* $RANDDIR
+
+cp $receptorTypes $RANDDIR
+NOMBRERECEPTOR=$(basename $receptorTypes)
+mv $RANDDIR/$NOMBRERECEPTOR $RANDDIR/receptor_atm_types.txt
+
+MYPWD=$PWD
+
+
+cd $RANDDIR
+
+source ADT_VENV/bin/activate
+
+(Rscript pdbcenter_npts_finder.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR) 2>&1
+
+(Rscript gpffilemaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR) 2>&1
+
+(Rscript glgfilemaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR) 2>&1
+
+echo "[INFO] Working path: $PWD"
+
+
+proteinPath=$PROTEINDB/$proteinCode
+echo "[INFO] - Extracting protein code [$proteinPath]"
+isRandomID="FALSE"
+if [ "$proteinCode" == "X__OC__PROTEINCODE__CC__" ]
+then
+	isRandomID="TRUE"
+	echo "No protein code supplied"
+fi
+
+filloutsNum=0
+filloutsAreGood=1
+if [ -d "$proteinPath" ] && [ $isRandomID == "FALSE" ]; then
+
+	for x in {10..600..10}
+	do
+	        filloutsNum=$(ls -lh $PROTEINDB/$proteinCode/FILL_${x}out* 2> /dev/null | wc -l)
+		if [ $filloutsNum -eq 0 ]; then
+			filloutsAreGood=0
+			echo "[INFO] Did not find fillout $x"
+		fi
+	done
+else
+	filloutsAreGood=0
+fi
+
+if [ -d "$proteinPath" ] && [ $filloutsAreGood -eq 1 ] && [ $isRandomID == "FALSE"  ]; then
+	echo "[INFO] Found protein in database. Reusing envelopes."
+	cp $proteinPath/FILL* .
+else
+	echo "[INFO] Did not find protein in database. Computing envelopes."
+	pathLigand=$(which AutoLigand.py)
+	(Rscript envelopesmaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR $pathLigand) 2>&1
+	mkdir $proteinPath
+	cp FILL* $proteinPath
+
+fi
+
+
+(Rscript clusterfilemaker.R $MYPWD/$RANDDIR) 2>&1
+
+(Rscript clusterfinder_Auto.R $MYPWD/$RANDDIR) 2>&1
+
+(Rscript cluster_to_vina_cluster.R $receptor_pdbqt_modified2 $ligand_pdbqt $out $log $size_x $MYPWD/$RANDDIR $receptor_name $ligand_name) 2>&1
+
+
+rm -rf ./CONDA_RDKIT_ENV
+rm -rf ./ADT_VENV
+
+cd $MYPWD
+
+
+deactivate