#!@SHELL@
#
# Uses molecuilder's DFS to find rings and creates map for sorting molecules first by atom number, then by number of rings and finally sorts the lines of the fail accordingly

exec_prefix="@prefix@"
database="@bindir@"
MOLECUILDER="@bindir@/molecuilder"

if [ -z $1 ]; then
	echo "Usage: $0 <file>"
	exit 1
else
	file=$1
fi

echo "Creating mapping ... "
echo -e "#Nr.\tMolecule\tNo.rings\tMinLength\tMaxLength\tAtoms" >MoleculesRing.dat
nr=1
for i in *.xyz; do 
	mol=${i/.xyz/}
	atoms=`head -n 1 $i | sed -e "s#\([0-9]*\).*#\1#"`
	echo "Current molecule: ${mol}" 
	echo -e -n "$nr\t$mol\t" >>MoleculesRing.dat
	rings=(`${MOLECUILDER} ${mol}/${mol}.conf  -e ${database} -c 5. 5. 5. -D 2. 2>/dev/null | grep -E "Found ring contains" | awk -F" of " {'print $2'} | awk -F"." {'print $1'}`)
	i=0
	Max=0
	Min=1000
	while [ $i -lt ${#rings[@]} ]; do
		if [ $Max -lt ${rings[$i]} ]; then
			Max=${rings[$i]}
		fi
		if [ $Min -gt ${rings[$i]} ]; then
			Min=${rings[$i]}
		fi
		let i=$i+1
	done
	if [ ! $Max -eq $Min ]; then		# there were no rings at all
		Min=0
	fi
	echo -e -n "${#rings[@]}\t$Max\t$Min\t$atoms\n" >>MoleculesRing.dat
	let nr=$nr+1
done
sort -g -t $'\t' +2 -3 +3n -4 +4n -5 +5n -6 MoleculesRing.dat > MoleculesRingSorted.dat

# now parsing file
rm -f ${file}_sorted
OLDIFS=$IFS
IFS='
'
lines=(`cat <$file`)
map=(`cat <MoleculesRingSorted.dat`)
i=0
while [ $i -lt ${#lines[@]} ]; do
	let j=`echo ${map[$i]}  | awk -F" " {'print $1'}`
	#echo "lines: ${lines[$i]}"
	#echo "Map: ${map[$i]} -> $i"
	name=`echo "${lines[$j]}" | awk -F" " {'print $1'}`
	echo -e -n "$name\t$i\t" >> ${file}_sorted
	echo "${lines[$j]}" | sed -e "s#[0-9a-zA-Z,_\-]*\t[0-9]*\t##" >>${file}_sorted
	let i=$i+1
done
IFS=$OLDIFS



exit 0