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

push my @molecules, quotemeta chomp while <MOL>;

$bigRegex = join '|', @molecules;

my $bigRegex;
($bigRegex .= join( '|', '\b'. $_ . '\b' ) ) for @molecules;

my $bigRegex;
$bigRegex = join '|', map { "\b$_\b" } sort { length $b <=> length $a 
+} @molecules;

#!/usr/bin/perl -w
use strict;
...
    print if( scalar( split /\t/ ) >= 6 
        && /^([^\t]*\t)?($bigRegex)/ );
}