for $i ( 1 .. $#allmolecules ) {
 ...

##</code><code>##

for my $currentMolecule ( @allmolecules ) {
   ... 
   while (my ($key,$val) = each  %$currentMolecule ) { #line 222
                  if (ref($val) eq "ARRAY")
                  {     print "$key=@$val"; }
                  else
                  {    print "$key=$val"; }

     ...
   }
}