Mercurial > repos > bitlab > plidflow
diff PLIDflow/launch_confmaker_multiple.sh @ 6:795e11fac81b draft default tip
Included new tools for standardization
author | bitlab |
---|---|
date | Wed, 22 Apr 2020 06:12:00 -0400 |
parents | |
children |
line wrap: on
line diff
--- /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