def add_staple_crossovers(design: sc.DNADesign):
for helix in range(23):
start_offset = 24 if helix % 2 == 0 else 40
for offset in range(start_offset, 296, 32):
if offset != 152: # skip crossover near seam
design.add_full_crossover(helix1=helix,
helix2=helix + 1,
offset1=offset,
forward1=helix % 2 == 1)
def add_crossovers(design: sc.DNADesign):
# staples interior
for offset in range(84, 1246, 42):
design.add_full_crossover(helix=0,
helix2=1,
offset=offset,
forward=False)
design.add_full_crossover(helix=3,
helix2=4,
offset=offset,
forward=True)
for offset in range(56, 1246, 42):
design.add_full_crossover(helix=1,
helix2=2,
offset=offset,
forward=True)
design.add_full_crossover(helix=4,
helix2=5,
offset=offset,
forward=False)
for offset in range(70, 1246, 42):
design.add_full_crossover(helix=2,
helix2=3,
offset=offset,
forward=False)
design.add_full_crossover(helix=5,
helix2=0,
offset=offset,
forward=True)
for offset in range(49, 1245,
42): # extra crossovers 5 - 0 for some reason
design.add_full_crossover(helix=5,
helix2=0,
offset=offset,
forward=True)
# staples edges
design.add_half_crossover(helix=0, helix2=1, offset=42, forward=False)
design.add_half_crossover(helix=3, helix2=4, offset=42, forward=True)
design.add_half_crossover(helix=0, helix2=5, offset=1245, forward=False)
design.add_half_crossover(helix=2, helix2=3, offset=1245, forward=False)
# scaffold interior
crossovers = []
for offset in range(58, 1250, 42):
crossovers.append(
sc.Crossover(helix=0, helix2=1, offset=offset, forward=True))
for offset in range(30, 1250, 42):
crossovers.append(
sc.Crossover(helix=1, helix2=2, offset=offset, forward=False))
for offset in range(54, 1250, 42):
crossovers.append(
sc.Crossover(helix=2, helix2=3, offset=offset, forward=True))
for offset in range(26, 1250, 42):
crossovers.append(
sc.Crossover(helix=3, helix2=4, offset=offset, forward=False))
# scaffold edges
crossovers.append(
sc.Crossover(helix=0, helix2=1, offset=16, forward=True, half=True))
crossovers.append(
sc.Crossover(helix=2, helix2=3, offset=12, forward=True, half=True))
crossovers.append(
sc.Crossover(helix=4, helix2=5, offset=19, forward=True, half=True))
crossovers.append(
sc.Crossover(helix=0, helix2=1, offset=1275, forward=True, half=True))
crossovers.append(
sc.Crossover(helix=2, helix2=3, offset=1271, forward=True, half=True))
crossovers.append(
sc.Crossover(helix=4, helix2=5, offset=1278, forward=True, half=True))
design.add_crossovers(crossovers)