open( MOL, "molecules" );
@molecules = <MOL>;
close MOL;
map { chomp; $_ = quotemeta; } @molecules;

$bigRegex = join '|', @molecules;

open( LOCUS, "locus" );
@locus = <LOCUS>;
close LOCUS;

foreach (@locus) {
    print if ( scalar( split /\t/ ) == 6 &&
               /^([^\t]+\t)?($bigRegex)/ );
}