Thanks -- those are mostly good points... except there's a problem in the second item:
I'd replace

   @molecules = <MOL>;
   map { chomp; $_ = quotemeta; } @molecules;
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with

   push my @molecules, quotemeta chomp while <MOL>;
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The problem with this replacement is that chomp simply modifies its arg ($_ in this case), but does not return the modified arg -- something other than the chomp'ed string gets returned to quotemeta, and pushed onto @molecules.

I just recently tried this sort of approach in an attempt to shorten a one-liner, and didn't get what you expect:

push @m, quotemeta chomp while <DATA>;
print join("|",@m),$/;
__DATA__
AAA
BBB
&*(
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Yields:

1|1|1

Maybe "map" in a void context isn't sexy, but it does work. (I agree that grep in a void context would be silly.)