Prototype vina script for resume support and error handling of multiple runs

vscript.sh

#!/bin/bash
echo "Short and simple VINA docking script - Jim"
echo ""
if [ $# -eq 0 ]
then    
        echo "Please enter the protein to dock (do not put the extension in): "
        read prot
fi   
if [ $# -eq 1 ]
then    
        prot="$1"
fi      
if [ $# -gt 1 ]
then    
        echo "Too many parameters!"
fi   
echo ""
echo "Protein: $prot"
decoys=`ls de*.pdbqt | wc -l`
ligands=`ls lg*.pdbqt | wc -l`
resumed="0"
resumel="0"
echo "Matching protein $prot with $decoys decoy(s) and $ligands ligand(s)..."
# Checks if conf file is identical, and if so, offers user opportunity to resume
if [ `grep "$prot" conf.txt | wc -l` -eq 1 ]
then
	#Find all subfolders that do NOT contain a *.pdbqt file
	#Thank you unix.com forums for this
	lastdecoy=`find . -type d -print0 | xargs -0 ./filecheck.sh | grep "de[0-9]*"`
  lastligand=`find . -type d -print0 | xargs -0 ./filecheck.sh | grep "lg[0-9]*"`
  #TODO: Put error condition when more than one directory is returned for each find
  #This indicates previous unstable terminations and should prompt user to wipe the whole directory
  #to prevent a corrupt state.
  if [ $lastdecoy ]
	then
  	lde=`basename $lastdecoy`
	fi
	if [ $lastligand ]
	then
  	llg=`basename $lastligand`
	fi
  if [ $lastdecoy ]
  then
  	echo "Would you like to resume at decoy $lde (y/n)?"
  	read answer
  elif [ $lastligand ]
  then
  	echo "Would you like to resume at ligand $llg (y/n)?"
  	read answer
  else
  	echo "It seems that a match has already completed in this directory."
	  # Delete previous match, on user request
		 echo "Would you like to completely start over (deleting all decoy and ligand directories) (y/n)?"
		 read answer2
		 if [ "$answer2" == "y" ] || [ "$answer2" == "Y" ]
	  	 then
	  			echo "Deleting ALL decoy directories..."
	  			rm -rf ./de*
	  			echo "Deleting ALL ligand directories..."
	  			rm -rf ./lg*
	  	 fi
  fi
  # Delete unfinished directories
  if [ "$answer" == "y" ] || [ "$answer" == "Y" ]
  then
	  #Delete last entry 
	  if [ ! -d /$lde ]
	  then
	  	if [ $lastdecoy ]
	  	then
		  	echo "Deleting unfinished decoy directory $lde..."
		  	rm -rf $lastdecoy
		  	resumed="1"
	  	fi
	  fi	
	  if [ ! -d /$llg ]
	  then
	  	if [ $lastligand ]
	  	then
		  	echo "Deleting unfinished ligand directory $llg..."
		  	rm -rf $lastligand
		  	resumel="1"
		  fi	
	  fi
	 else
	   echo "Would you like to completely start over (deleting all decoy and ligand directories) (y/n)?"
	   if [ "$answer" == "y" ] || [ "$answer" == "Y" ]
  	 then
  			echo "Deleting ALL decoy directories..."
  			rm -rf ./de*
  			echo "Deleting ALL ligand directories..."
  			rm -rf ./lg*
  	 fi		
   fi
   for f in de*.pdbqt; do
	    b=`basename $f .pdbqt`
	    if [ $resumed -eq 1 ]
	    then
	    	if [ "$lde" == "$b" ]
	    	then
	    		resumed="0"
	    		echo Processing de $b
			    mkdir -p $b
			    ./vina --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt
			  else
			  	echo "Skipping de $b"
	    	fi
	    else  				
		    echo Processing de $b
		    mkdir -p $b
		    ./vina --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt
	    fi
	 done
	 for f in lg*.pdbqt; do
	    b=`basename $f .pdbqt`
	    if [ $resumel -eq 1 ]
	    then
	    	if [ "$llg" == "$b" ]
	    	then
	    		resumel="0"
	    		echo Processing lg $b
			    mkdir -p $b
			    ./vina --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt
			  else
			  	echo "Skipping de $b"
	    	fi
	    else  				
		    echo Processing lg $b
		    mkdir -p $b
		    ./vina --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt
	    fi
	 done
# New protein, starting over
# NOT TESTED YET
else
	echo "A match already exists here. Delete previous results (y/n)?"
	echo "You can take the time to back them up now if you want."
	read answer
	if [ "$answer2" == "y" ] || [ "$answer2" == "Y" ]
	then
		echo "Deleting ALL decoy directories..."
		rm -rf ./de*
		echo "Deleting ALL ligand directories..."
		rm -rf ./lg*
  fi
  sed -e 's/receptor = .*\.pdbqt/receptor = $prot\.pdbqt/g' conf.txt > conftemp.txt
  rm conf.txt.bak
  mv conf.txt conf.txt.bak
  mv conftemp.txt conf.txt
  echo "Starting new match with $prot..."
  for f in de*.pdbqt; do
	    b=`basename $f .pdbqt`
	    echo Processing de $b
	    mkdir -p $b
	    ./vina --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt
	done
	for f in lg*.pdbqt; do
	    b=`basename $f .pdbqt`
	    echo Processing lg $b
	    mkdir -p $b
	    ./vina --config conf.txt --ligand $f --out ${b}/out.pdbqt --log ${b}/log.txt
	done		
fi