def domain_end(design: sc.Design, helix,
offset): #True if it is a domain end or if nothing exists
if len(design.domains_at(helix, offset)) == 2:
if design.domains_at(helix, offset)[0].start == offset or \
design.domains_at(helix, offset)[0].end == offset or \
design.domains_at(helix, offset)[1].start == offset or \
design.domains_at(helix, offset)[1].end == offset :
return True
else:
return False
elif len(design.domains_at(helix, offset)) == 1:
if design.domains_at(helix, offset)[0].start == offset or \
design.domains_at(helix, offset)[0].end == offset :
return True
else:
return False
else:
return True #since we don't want crossovers where nothing exists
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 valid_deletion_offset(design: sc.Design, helix: int, offset: int) -> bool:
domains_at_offset = design.domains_at(helix, offset)
if len(domains_at_offset) > 2:
raise ValueError(f'Invalid Design; more than two Substrands found at '
f'helix {helix} and offset {offset}: '
f'{domains_at_offset}')
elif len(domains_at_offset) != 2:
return False
for ss in domains_at_offset:
if offset in ss.deletions:
return False # already a deletion there
if offset in (insertion[0] for insertion in ss.insertions):
return False # already an insertion there
if offset == ss.start:
return False # no 5' end
if offset == ss.end - 1:
return False # no 3' end
return True
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)
