def add_scaffold_nicks(design: sc.DNADesign):
for helix in range(1, 24):
design.add_nick(helix=helix, offset=152, forward=helix % 2 == 0)
def add_nicks(design: sc.DNADesign):
design.add_nick(helix=5, offset=399, forward=False) # scaffold
for offset in range(56, 1246, 42):
design.add_nick(helix=0, offset=offset, forward=False)
design.add_nick(helix=3, offset=offset, forward=True)
for offset in range(70, 1246, 42):
design.add_nick(helix=1, offset=offset, forward=True)
design.add_nick(helix=4, offset=offset, forward=False)
for offset in range(84, 1246, 42):
design.add_nick(helix=2, offset=offset, forward=False)
design.add_nick(helix=5, offset=offset, forward=True)
def add_staple_nicks(design: sc.DNADesign):
for helix in range(24):
start_offset = 32 if helix % 2 == 0 else 48
for offset in range(start_offset, 280, 32):
design.add_nick(helix, offset, forward=helix % 2 == 1)