def add_domains_for_barrel_seam(design: sc.Design) -> None:
top_staples_5p = design.strands_starting_on_helix(2)
top_staples_3p = design.strands_ending_on_helix(2)
bot_staples_5p = design.strands_starting_on_helix(17)
bot_staples_3p = design.strands_ending_on_helix(17)
# 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=2,
forward=False,
start=top_5p.first_domain().end,
end=top_3p.last_domain().start)
ss_bot = sc.Domain(helix=17,
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.Design):
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 assign_dna_to_unzipper_toeholds(design: sc.Design) -> None:
uz_toes = [sc.wc(seq) for seq in uz_toes_wc]
strands_h1 = design.strands_starting_on_helix(1)
strands_h1.sort(key=lambda _strand: _strand.first_domain().offset_5p())
strands_h1.reverse()
strands_h18 = design.strands_starting_on_helix(18)
strands_h18.sort(key=lambda _strand: _strand.first_domain().offset_5p())
for strand, toe in zip(strands_h1 + strands_h18, uz_toes):
seq = toe + sc.DNA_base_wildcard * (strand.dna_length() - 8)
design.assign_dna(strand, seq)
def add_deletions(design: sc.Design):
for helix in range(3, maxhelix):
if not design.strands_starting_on_helix(helix):
pass
else:
hel1 = helix #first starting helix
break
for helix in range(hel1, maxhelix, 2):
for offset in range(block * cmax):
if design.domains_at(helix, offset) and offset % 48 == 0:
design.add_deletion(helix, offset)
def add_toeholds_for_seam_displacement(design: sc.Design) -> None:
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_bound_domain().start,
end=stap_5p.first_bound_domain().end)
design.insert_domain(stap_5p, 0, toe_ss)
def add_scaffold_nicks(design: sc.Design):
crossovers = []
for helix in range(3, maxhelix, 2):
if not design.strands_starting_on_helix(helix):
pass
else:
hel1 = helix #first starting helix
break
for helix in range(hel1, maxhelix, 2):
scafdom1 = design.strands_starting_on_helix(helix)
scafdom2 = design.strands_starting_on_helix(helix + 1)
if not (scafdom1
and scafdom2): #check for empty helix at the end of the design
break
imghelix = int((helix - 1) / 2)
if (1 in img[imghelix]) and (1 in img[imghelix + 1]):
interstarts = []
interends = []
for dom in range(1, len(img[imghelix])):
if (bool(img[imghelix][dom] and img[imghelix+1][dom])) and \
(not bool(img[imghelix][dom-1] and img[imghelix+1][dom-1])):
interstarts.append(dom)
if (not bool(img[imghelix][dom] and img[imghelix+1][dom])) and \
(bool(img[imghelix][dom-1] and img[imghelix+1][dom-1])):
interends.append(dom)
interstarts = [x * block for x in interstarts]
interends = [x * block for x in interends]
for i in range(len(interstarts)):
#finds the scaffold crossover offset position 'nickoff', for the square lattice,
#closest to the center of the intersection of helices that are crossing over
closestoff = int((interstarts[i] + interends[i]) / 2) - 2
closerem = (closestoff) % 32
if (closerem < 10):
nickoff = 3 + 32 * int(closestoff / 32)
if nickoff <= interstarts[i]:
nickoff = 3 + 32 * int(closestoff / 32) + 10
elif nickoff >= interends[i]:
nickoff = 3 + 32 * int(closestoff / 32) - 11
elif (closerem > 10) and (closerem < 21):
nickoff = 3 + 32 * int(closestoff / 32) + 10
if nickoff <= interstarts[i]:
nickoff = 3 + 32 * int(closestoff / 32) + 21
elif nickoff >= interends[i]:
nickoff = 3 + 32 * int(closestoff / 32)
elif (closerem > 21) and (closerem < 32):
nickoff = 3 + 32 * int(closestoff / 32) + 21
if nickoff <= interstarts[i]:
nickoff = 3 + 32 * int(closestoff / 32) + 32
elif nickoff >= interends[i]:
nickoff = 3 + 32 * int(closestoff / 32) + 10
else:
nickoff = 3 + 32 * int(closestoff / 32) + closerem
design.add_nick(helix=helix,
offset=nickoff,
forward=helix % 2 == 0)
design.add_nick(helix=helix + 1,
offset=nickoff,
forward=helix % 2 == 1)
crossovers.append(
sc.Crossover(helix=helix,
helix2=helix + 1,
offset=nickoff,
forward=False))
design.add_nick(helix=helix, offset=nickoff, forward=helix % 2 == 0)
design.add_crossovers(crossovers)
def add_staple_nicks(design: sc.Design):
crossovers = []
for helix in range(3, maxhelix, 2):
if not design.strands_starting_on_helix(helix):
pass
else:
hel1 = helix #first starting helix
break
for helix in range(hel1, maxhelix, 2):
scafdom1 = design.strands_starting_on_helix(helix)
scafdom2 = design.strands_starting_on_helix(helix + 1)
if not (scafdom1
and scafdom2): #check for empty helix at the end of the design
break
for helix in range(maxhelix):
if helix % 2 == 0:
for offset in range(block * cmax):
if (offset % 32 == 0) and (design.domains_at(helix, offset)):
if domain_end(design, helix,
offset): #no nick if domain end
continue
#Prevent very short staples
if (design.domains_at(helix, offset-16)) and \
(design.domains_at(helix, offset+16)):
design.add_nick(helix=helix,
offset=offset,
forward=helix % 2 == 1)
if 0<=(offset-8)<=block*cmax and \
(design.domains_at(helix, offset-16)) and \
(design.domains_at(helix, offset)) and \
(design.domains_at(helix+1, offset-8)) and \
(design.domains_at(helix+1, offset-9)) and \
not domain_end(design, helix, offset-8):
crossovers.append(sc.Crossover(helix=helix, helix2=helix + 1, \
offset=offset-8, forward=helix % 2 == 1))
else:
for offset in range(block * cmax):
if ((offset + 16) % 32 == 0) and (design.domains_at(
helix, offset)):
if domain_end(design, helix, offset):
continue
#Prevent very short staples
if (design.domains_at(helix, offset-16)) and \
(design.domains_at(helix, offset+16)):
design.add_nick(helix=helix,
offset=offset,
forward=helix % 2 == 1)
if 0<=(offset-8)<=block*cmax and \
(design.domains_at(helix, offset-16)) and \
(design.domains_at(helix, offset)) and \
(design.domains_at(helix+1, offset-8)) and \
(design.domains_at(helix+1, offset-9)) and \
not domain_end(design, helix, offset-8):
crossovers.append(sc.Crossover(helix=helix, helix2=helix + 1, \
offset=offset-8, forward=helix % 2 == 1))
design.add_crossovers(crossovers)
def add_staple_nicks(design: sc.Design):
crossovers = []
midgap = 3
state = 0
every = -1 #skip every xth crossover
for helix in range(3, maxhelix, 2):
if not design.strands_starting_on_helix(helix):
pass
else:
hel1 = helix #first starting helix
break
for helix in range(hel1, maxhelix, 2):
scafdom1 = design.strands_starting_on_helix(helix)
scafdom2 = design.strands_starting_on_helix(helix + 1)
if not (scafdom1
and scafdom2): #check for empty helix at the end of the design
break
for helix in range(maxhelix):
if helix % 2 == 0:
for offset in range(block * cmax):
if (((offset-3)%32==0) or \
((offset-3)%32==10) or \
((offset-3)%32==21)) and \
(design.domains_at(helix, offset+midgap)):
state = state + 1
if not every == -1:
if state % every == 0:
# print(str(helix)+' '+str(offset))
continue
if domain_end(design, helix,
offset + midgap): #no nick if domain end
continue
#Prevent very short staples
if long_stap_cond(design, helix, offset + midgap) == True:
design.add_nick(helix=helix,
offset=offset + midgap,
forward=helix % 2 == 1)
if cross_conds(design, helix, offset):
crossovers.append(sc.Crossover(helix=helix, helix2=helix + 1, \
offset=offset, forward=helix % 2 == 1))
elif helix == 2:
print("not here " + str(offset))
else:
for offset in range(block * cmax):
if (((offset-8)%32==0) or \
((offset-8)%32==11) or \
((offset-8)%32==21)) and \
(design.domains_at(helix, offset+midgap)):
state = state + 1
if not every == -1:
if state % every == 0:
# print(str(helix)+' '+str(offset))
continue
if domain_end(design, helix,
offset + midgap): #no nick if domain end
continue
# #Prevent very short staples
# if long_stap_cond(design, helix, offset+midgap)==True:
# design.add_nick(helix=helix, offset=offset+midgap, forward=helix % 2 == 1)
if cross_conds(design, helix, offset):
crossovers.append(sc.Crossover(helix=helix, helix2=helix + 1, \
offset=offset, forward=helix % 2 == 1))
design.add_crossovers(crossovers)