while getopts ":f:o:c:" opt; do
  flags=1
  case $opt in
    f)
      inputfile=$OPTARG
      ;;
    o)
      outputfile=$OPTARG
      ;;
    c)
      if [[ $OPTARG == "" ]]
      then
      	consec=0
      else
      consec=$OPTARG
      fi
      ;;
    \?)
      echo "Invalid option: -$OPTARG" >&2
      exit
      ;;
  esac
done


if [[ $flags == "" ]]
then
	echo "Usage: PDBid_change -f -o [-c]"
	echo "-f input file name"
	echo "-o output file name"
	echo "-c start id from 0 or value"
	exit
fi

if [[ $inputfile == "" ]]
then
	echo "Please provide an input file name (-f filename)"
	exit
else
	if ! [[ -e "$inputfile" ]]
	then
		echo "Input file does not exits"
		exit
	fi
fi

if [[ $outputfile == "" ]]
then
	echo "Please provide an output file name (-o filename)"
	exit
fi

cat /dev/null > $outputfile


function write_pdb() {
if  [[ ${#newid} == ${#position} ]]
then
	if  [[ ${#newid} == 1 ]]
	then
		echo "$line" | sed "s/A   $id/A   $newid/" >> $1
	elif [[ ${#newid} == 2 ]]
	then
		echo "$line" | sed "s/A  $id/A  $newid/" >> $1
	elif [[ ${#newid} == 3 ]]
	then
		echo "$line" | sed "s/A $id/A $newid/" >> $1
	else
		echo "$line" | sed "s/A$id/A$newid/" >> $1
	fi
elif [[ ${#newid} == 1 && ${#position} == 2 ]]
then
	echo "$line" | sed "s/A  $id/A   $newid/" >> $1
elif [[ ${#newid} == 1 && ${#position} == 3 ]]
then
	echo "$line" | sed "s/A $id/A   $newid/" >> $1
elif [[ ${#newid} == 1 && ${#position} == 4 ]]
then
	echo "$line" | sed "s/A$id/A   $newid/" >> $1
elif [[ ${#newid} == 2 && ${#position} == 3 ]]
then
	echo "$line" | sed "s/A $id/A  $newid/" >> $1
elif [[ ${#newid} == 2 && ${#position} == 4 ]]
then
	echo "$line" | sed "s/A$id/A  $newid/" >> $1
else
	echo "$line" | sed "s/A$id/A $newid/" >> $1
fi
}


cat $inputfile | while read line; do 

	atom=`echo $line | awk '{ print $1 }'`
	if  [[ "$atom" != "ATOM" && "$atom" != "TER" ]] 
	then
		echo "$line" >> $outputfile
	else
	 	
	 	if  [[ "$position" == "" ]]
	  	then
	  	position=`echo $line | awk '{ print $6 }'`
	  		if [[ "$consec" != "" ]]
	  		then
      		previous=$consec
      		else
      		previous=`echo $line | awk '{ print $6 }'`-5
      		fi      		
     	fi
     	
     	id=`echo $line | awk '{ print $6 }'`
     	if  [[ "$position" == "$id" ]]
     	then
     		newid=$[$previous+1]
     		write_pdb $outputfile
       	elif [ $atom == "TER" ]
     	then
     		id=`echo $line | awk '{ print $5 }'`
     		write_pdb $outputfile
      	else
      		previous=$newid
      		position=$id
      		newid=$[$previous+1]
      		write_pdb $outputfile     		
      	fi
	fi
done