Pinyili2

See merge request !1

Use graph methods to compute location of bead in _other_ segments for better performance; update some development logger messages

Make generate_bead_model use one_bead_per_monomer=True by default with max 1 bead per nt and bp, otherwise False

Order of double-stranded segment creation and ds-segment direction should match original cadnano reader.
Position and orientation of cadnano bases more consistent with original cadnano reader.