def add_scaffold_crossovers(design: sc.Design):
crossovers = []
# scaffold edges
for helix in range(len(img)):
if (1 in img[helix]):
for dom in range(len(img[helix])):
if (img[helix][dom] == 1) and (img[helix][dom - 1] == 0):
start = block * dom
if (img[helix][dom] == 0) and (img[helix][dom - 1] == 1):
end = block * dom
crossovers.append(
sc.Crossover(helix=2 * helix,
helix2=2 * helix + 1,
offset=start,
forward=True,
half=True))
crossovers.append(
sc.Crossover(helix=2 * helix,
helix2=2 * helix + 1,
offset=end - 1,
forward=True,
half=True))
design.add_crossovers(crossovers)
def add_scaffold_crossovers(design: sc.DNADesign):
crossovers = []
# scaffold interior
for helix in range(1, 23, 2):
crossovers.append(
sc.Crossover(helix1=helix,
helix2=helix + 1,
offset1=152,
forward1=False))
# scaffold edges
for helix in range(0, 23, 2):
crossovers.append(
sc.Crossover(helix1=helix,
helix2=helix + 1,
offset1=8,
forward1=True,
half=True))
crossovers.append(
sc.Crossover(helix1=helix,
helix2=helix + 1,
offset1=295,
forward1=True,
half=True))
design.add_crossovers(crossovers)
def add_crossovers(design: sc.Design, crossover_list, scaffold_or_staple):
"""Adds crossovers"""
crossovers = []
for helix in range(len(crossover_list)):
if crossover_list[helix] == 'no crossover':
continue
else:
for crossover in crossover_list[helix]:
helix2 = crossover[1]
offset = crossover[2]
offset2 = crossover[3]
forward = sc_general.forward_strand(helix, scaffold_or_staple)
forward2 = sc_general.forward_strand(helix2, scaffold_or_staple)
crossovers.append(sc.Crossover(helix = helix, helix2 = helix2, offset = offset, offset2 = offset2, forward = forward, forward2 = forward2, half = True))
design.add_crossovers(crossovers)
def add_adaptor_crossovers(design):
"""Given a adaptor design, adds the crossovers"""
crossovers = []
croosover_locations = [16, 36, 37]
for helix in range(1, 12, 2):
if helix == 11:
helix2 = 0
else:
helix2 = helix + 1
forward = sc_general.forward_strand(helix, 'staple')
forward2 = sc_general.forward_strand(helix2, 'staple')
for offset in croosover_locations:
crossovers.append(
sc.Crossover(helix=helix,
helix2=helix2,
offset=offset,
offset2=offset,
forward=forward,
forward2=forward2,
half=True))
design.add_crossovers(crossovers)
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)
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)
def add_hairpins(design, hairpin_locations, hairpin_lattice):
"""Given the design, the hairpin lattice, and the hairpin locations, adds the hairpins to the hairpin lattice and crossovers to the seed"""
seed_domain = range(len(hairpin_locations))
hairpin_domain = range(len(hairpin_locations),
len(hairpin_locations) + len(hairpin_lattice))
#creates the hairpins, included the loopout crossover
for i in range(len(hairpin_domain)):
helix = hairpin_domain[i]
for j in range(len(hairpin_locations[helix - len(seed_domain)])):
left_offset = hairpin_locations[helix - len(seed_domain)][j]
right_offset = left_offset + 8
index = 6 * (i - 1) + j
pin_seq = non_random_hairpin_sequence(index)
staple = sc.Strand([
sc.Domain(helix=helix,
forward=True,
start=left_offset,
end=right_offset),
sc.Loopout(length=4),
sc.Domain(helix=helix,
forward=False,
start=left_offset - 2,
end=right_offset)
],
dna_sequence=pin_seq)
design.add_strand(staple)
#add nicks on staple strands to be able to connect the hairpins
for helix in seed_domain:
forward = sc_general.forward_strand(helix, 'staple')
for nick in hairpin_locations[helix]:
design.add_nick(helix=helix, offset=nick, forward=forward)
#crossovers between the main helices and the hairpins
crossovers = []
for helix in seed_domain:
helix2 = hairpin_domain[helix]
forward = sc_general.forward_strand(helix, 'staple')
for pin in hairpin_locations[helix]:
if forward == True:
forward_pin_offset = pin - 1
reverse_pin_offset = pin
else:
forward_pin_offset = pin
reverse_pin_offset = pin - 1
crossovers.append(
sc.Crossover(helix=helix,
helix2=helix2,
offset=forward_pin_offset,
offset2=pin,
forward=forward,
forward2=True,
half=True))
crossovers.append(
sc.Crossover(helix=helix,
helix2=helix2,
offset=reverse_pin_offset,
offset2=pin - 2,
forward=forward,
forward2=False,
half=True))
design.add_crossovers(crossovers)