#!/bin/bash

ROOT=$1
SUF=$2

MASK="$ROOT"'_*.'$SUF'.in'
R=$RANDOM
S=2
B=1

i=$B
for mol in $(grep 'Energy =' $MASK | sort -k 4 -n | cut -f 1 -d ':') ;
do
  mv -vi $mol "$ROOT"_$(printf "%0"$S"d\n" $i)."$SUF".in"$R"
  i=$(($i+1))
done

for mol in *.in"$R"
do
  mv -vi $mol ${mol/$R}
done