def add_scaffold_nicks(design: sc.Design, seam_locations):
"""Adds nicks to the precursor scaffold"""
for helix in range(len(seam_locations)):
if seam_locations[helix] == 'no seam':
continue
else:
nick_offsets = seam_locations[helix]
for nick_offset in nick_offsets:
if nick_offset != 'no seam':
forward = sc_general.forward_strand(helix, 'scaffold')
design.add_nick(helix = helix, offset = nick_offset, forward = forward)
def add_nicks(design: sc.Design) -> None:
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_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_scaffold_nicks(design: sc.Design):
for helix in range(1, 24):
design.add_nick(helix=helix, offset=152, forward=helix % 2 == 0)
def add_staple_nicks(design: sc.Design):
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)
def add_staple_nicks(design: sc.Design) -> None:
for helix in range(24):
start_offset = 24 if helix % 2 == 0 else 40
for offset in range(start_offset, 272, 32):
design.add_nick(helix, offset, forward=helix % 2 == 1)
def add_staple_nicks(design: sc.Design, nick_locations):
"""Adds nicks ot the precursor staple strands"""
for helix in range(len(nick_locations)):
forward = sc_general.forward_strand(helix, 'staple')
for nick in nick_locations[helix]:
design.add_nick(helix = helix, offset = nick, forward = forward)
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)
