Updated interhelical bond exclusions to be consistent with ENRG MD server; no bonds within 10 angstroms of crossover

Fixed how atoms are indexed to allow interhelical bonds when insertions/deletions are staggered; generalized algorithms for finding indices between crossovers

Updated orientation of ssDNA in atomic model so that z-axis is aligned with vector connecting adjacent nts; untested

Fixed beadModel neighborhood algorithm; Added atomicModel support for looped structures; Added methods for breaking bonds beyond a certain length