circular Strands

[dave-doty]

Add a Boolean field Strand.circular and draw a crossover from last substrand to first. Any equivalent cyclic permutation of the substrands should display in the same way.

Even if one doesn't wish the final design to have circular strands, this will help to avoid the problem that sometimes an intermediate design temporarily creates a circular Strand, even though subsequent edits make it linear again. Currently such designs are simply not allowed.

See UC-Davis-molecular-computing/scadnano#5.

[dave-doty]

[BREAKING CHANGE] Since circular strands make it easier to use the Design.add_half_crossover and Design.add_full_crossover methods, we have removed the method Design.add_crossovers and the type Crossover. Previously, that method helped avoid creating circular strands by allowing one to build up a list of Crossovers and add them in bulk, where adding them one at a time would have resulted in an intermediate circular strand, even if the final result had all linear strands. Now that circular strands are supported, this is no longer needed. The recommended method of adding many crossovers at once is simply to call Design.add_half_crossover and/or Design.add_full_crossover repeatedly, i.e., replace

crossovers = [
    Crossover(helix=0, helix2=1, offset=16, forward=True, half=True),
    Crossover(helix=0, helix2=1, offset=24, forward=False, half=True),
    Crossover(helix=2, helix2=3, offset=32, forward=True),
    Crossover(helix=2, helix2=3, offset=40, forward=False),
]
design.add_crossovers(crossovers)

with this instead:

design.add_half_crossover(helix=0, helix2=1, offset=16, forward=True)
design.add_half_crossover(helix=0, helix2=1, offset=24, forward=False)
design.add_full_crossover(helix=2, helix2=3, offset=32, forward=True)
design.add_full_crossover(helix=2, helix2=3, offset=40, forward=False)