store StrandPair instead of Tuple[Strand, Strand] in ConstraintWithStrandPairs and make _determine_strand_pairs_to_check more efficient

[dave-doty]

Profiling shows a lot of time is spent here. Seems like this part could be changed from quadratic to linear:

        if constraint.pairs is not None:
            for strand1, strand2 in constraint.pairs:
                for domain_changed in domains_changed:
                    if domain_changed in strand1.domains or domain_changed in strand2.domains:
                        strand_pairs_to_check.append(StrandPair(strand1, strand2))
                        break  # ensure we don't add the same strand pair twice