#!/bin/bash

f=${1/\.in}
f=${f/\.out}
if [ ! -e $f.out ]       ; then echo 'file?' ; exit 1 ; fi
if grep -q 'MOL>' $f.out ; then echo 'mol!'  ; exit 1 ; fi

lines=$(grep 'mol>' -c $f.out)
mols=$(grep 'mol>$molecule' -c $f.out)
n=$(($lines/$mols))
bra=$(($mols*$n-$n+1))

mv $f.{in,bak}
sed -n -e '/$molecule/q' -e p  $f.bak  > $f.in
grep 'mol>' $f.out | sed -n "$bra,\$p" | sed 's/mol>//' >> $f.in
diff $f.{bak,in} | tail