def add_domains_for_barrel_seam(design: sc.DNADesign):
top_staples_5p = design.strands_starting_on_helix(0)
top_staples_3p = design.strands_ending_on_helix(0)
bot_staples_5p = design.strands_starting_on_helix(15)
bot_staples_3p = design.strands_ending_on_helix(15)
# remove scaffold
top_staples_5p = [st for st in top_staples_5p if len(st.domains) <= 3]
top_staples_3p = [st for st in top_staples_3p if len(st.domains) <= 3]
bot_staples_5p = [st for st in bot_staples_5p if len(st.domains) <= 3]
bot_staples_3p = [st for st in bot_staples_3p if len(st.domains) <= 3]
top_staples_5p.sort(key=lambda stap: stap.offset_5p())
top_staples_3p.sort(key=lambda stap: stap.offset_3p())
bot_staples_5p.sort(key=lambda stap: stap.offset_5p())
bot_staples_3p.sort(key=lambda stap: stap.offset_3p())
for top_5p, top_3p, bot_5p, bot_3p in zip(top_staples_5p, top_staples_3p,
bot_staples_5p, bot_staples_3p):
ss_top = sc.Domain(helix=0,
forward=False,
start=top_5p.first_domain().end,
end=top_3p.last_domain().start)
ss_bot = sc.Domain(helix=15,
forward=True,
start=bot_3p.last_domain().end,
end=bot_5p.first_domain().start)
design.insert_domain(bot_5p, 0, ss_top)
design.insert_domain(top_5p, 0, ss_bot)
def move_top_and_bottom_staples_within_column_boundaries(design: sc.DNADesign):
top_staples = design.strands_starting_on_helix(0)
bot_staples = design.strands_starting_on_helix(15)
bot_staples.remove(design.scaffold)
for top_staple in top_staples:
current_end = top_staple.domains[0].end
design.set_end(top_staple.domains[0], current_end - 8)
for bot_staple in bot_staples:
current_start = bot_staple.domains[0].start
design.set_start(bot_staple.domains[0], current_start + 8)
def add_toeholds_for_seam_displacement(design: sc.DNADesign):
for helix in [2, 17]:
staples_5p = design.strands_starting_on_helix(helix)
# remove scaffold
staples_5p = [st for st in staples_5p if len(st.domains) <= 3]
staples_5p.sort(key=lambda stap: stap.offset_5p())
for stap_5p in staples_5p:
toe_ss = sc.Domain(helix=1 if helix == 2 else 18, forward=helix == 2,
start=stap_5p.first_domain().start, end=stap_5p.first_domain().end)
design.insert_domain(stap_5p, 0, toe_ss)