in reply to Re^3: using s/// as map?
in thread how can I speed up this perl??

You're only doing half the work now :-)
But if I understand gene work (not a certainty at all), I'm doing the half they actually want to do. :-P A molecule isn't paired with both of its neighbors, they are grouped two-by-two.

At least now I understand why they were doing the lookahead.

The PerlMonks advocate for tr///