def add_adapters(design):
# left adapters
left_inside_seed = 48
left_outside_seed = left_inside_seed - 26
for bot_helix in range(2, 18, 2):
top_helix = bot_helix - 1 if bot_helix != 2 else 17
ss_top = sc.Domain(helix=top_helix,
forward=True,
start=left_outside_seed,
end=left_inside_seed)
ss_bot = sc.Domain(helix=bot_helix,
forward=False,
start=left_outside_seed,
end=left_inside_seed)
idt = sc.IDTFields(name=f'adap-left-{top_helix}-{bot_helix}',
scale='25nm',
purification='STD')
adapter = sc.Strand(domains=[ss_bot, ss_top], idt=idt)
design.add_strand(adapter)
# right adapters
right_inside_seed = 464
right_outside_seed = right_inside_seed + 26
for bot_helix in range(2, 18, 2):
top_helix = bot_helix - 1 if bot_helix != 2 else 17
ss_top = sc.Domain(helix=top_helix,
forward=True,
start=right_inside_seed,
end=right_outside_seed)
ss_bot = sc.Domain(helix=bot_helix,
forward=False,
start=right_inside_seed,
end=right_outside_seed)
idt = sc.IDTFields(name=f'adap-right-{top_helix}-{bot_helix}',
scale='25nm',
purification='STD')
adapter = sc.Strand(domains=[ss_top, ss_bot], idt=idt)
design.add_strand(adapter)
def main():
num_strands = 208
start = 0
strands = []
plate = 1
row_idx = 0
col_idx = 0
for s in range(1, num_strands + 1):
ss_f = sc.Domain(helix=0, forward=True, start=start, end=start + 10)
ss_r = sc.Domain(helix=1, forward=False, start=start, end=start + 10)
row = ROWS[row_idx]
col = COLS[col_idx]
well = f'{row}{col}'
idt = sc.IDTFields(name=f"staple{s}", plate=f'plate{plate}', well=well)
strand = sc.Strand(domains=[ss_f, ss_r], idt=idt)
strands.append(strand)
row_idx += 1
if row_idx == len(ROWS):
row_idx = 0
col_idx += 1
if col_idx == len(COLS):
col_idx = 0
plate += 1
start += 10
scaffold = sc.Strand([
sc.Domain(helix=0, forward=False, start=0, end=start),
sc.Domain(helix=1, forward=True, start=0, end=start)
],
is_scaffold=True)
strands.append(scaffold)
design = sc.DNADesign(strands=strands, grid=sc.square)
design.assign_m13_to_scaffold()
return design
def main():
width = 6
width_h = width // 2
stap_left_ss1 = sc.Domain(1, sc.forward, 0, width_h)
stap_left_ss0 = sc.Domain(0, sc.reverse, 0, width_h)
stap_right_ss0 = sc.Domain(0, sc.reverse, width_h, width)
stap_right_ss1 = sc.Domain(1, sc.forward, width_h, width)
scaf_ss1_left = sc.Domain(1, sc.reverse, 0, width_h)
scaf_ss0 = sc.Domain(0, sc.forward, 0, width)
scaf_ss1_right = sc.Domain(1, sc.reverse, width_h, width)
stap_left = sc.Strand([stap_left_ss1, stap_left_ss0])
stap_right = sc.Strand([stap_right_ss0, stap_right_ss1])
scaf = sc.Strand([scaf_ss1_left, scaf_ss0, scaf_ss1_right],
color=sc.default_scaffold_color)
strands = [stap_left, stap_right, scaf]
design = sc.DNADesign(strands=strands, grid=sc.square)
design.add_deletion(helix=0, offset=1)
design.add_deletion(helix=0, offset=4)
design.add_deletion(helix=1, offset=1)
design.add_deletion(helix=1, offset=4)
design.assign_dna(scaf, 'AACATCGT')
return design
def create_design():
# helices
helices = [sc.Helix(max_offset=48), sc.Helix(max_offset=48)]
# left staple
stap_left_ss1 = sc.Domain(helix=1, forward=True, start=8, end=24)
stap_left_ss0 = sc.Domain(helix=0, forward=False, start=8, end=24)
stap_left = sc.Strand(domains=[stap_left_ss1, stap_left_ss0])
# right staple
stap_right_ss0 = sc.Domain(helix=0, forward=False, start=24, end=40)
stap_right_ss1 = sc.Domain(helix=1, forward=True, start=24, end=40)
stap_right = sc.Strand(domains=[stap_right_ss0, stap_right_ss1])
# scaffold
scaf_ss1_left = sc.Domain(helix=1, forward=False, start=8, end=24)
scaf_ss0 = sc.Domain(helix=0, forward=True, start=8, end=40)
loopout = sc.Loopout(length=3)
scaf_ss1_right = sc.Domain(helix=1, forward=False, start=24, end=40)
scaf = sc.Strand(
domains=[scaf_ss1_left, scaf_ss0, loopout, scaf_ss1_right],
is_scaffold=True)
# whole design
design = sc.Design(helices=helices,
strands=[scaf, stap_left, stap_right],
grid=sc.square)
# deletions and insertions added to design are added to both strands on a helix
design.add_deletion(helix=1, offset=20)
design.add_insertion(helix=0, offset=14, length=1)
design.add_insertion(helix=0, offset=26, length=2)
# also assigns complement to strands other than scaf bound to it
design.assign_dna(scaf, 'AACGT' * 18)
return design
def main():
# left staple
stap_left_ss1 = sc.Domain(helix=1, forward=True, start=0, end=16)
stap_left_ss0 = sc.Domain(helix=0, forward=False, start=0, end=16)
stap_left = sc.Strand(domains=[stap_left_ss1, stap_left_ss0])
# right staple
stap_right_ss0 = sc.Domain(helix=0, forward=False, start=16, end=32)
stap_right_ss1 = sc.Domain(helix=1, forward=True, start=16, end=32)
stap_right = sc.Strand(domains=[stap_right_ss0, stap_right_ss1])
# scaffold
scaf_ss1_left = sc.Domain(helix=1, forward=False, start=0, end=16)
scaf_ss0 = sc.Domain(helix=0, forward=True, start=0, end=32)
loopout = sc.Loopout(length=3)
scaf_ss1_right = sc.Domain(helix=1, forward=False, start=16, end=32)
scaf = sc.Strand(
domains=[scaf_ss1_left, scaf_ss0, loopout, scaf_ss1_right],
is_scaffold=True)
# whole design
design = sc.DNADesign(strands=[scaf, stap_left, stap_right],
grid=sc.square)
# deletions and insertions added to design so they can be added to both strands on a helix
design.add_deletion(helix=0, offset=11)
design.add_deletion(helix=0, offset=12)
design.add_deletion(helix=0, offset=24)
design.add_deletion(helix=1, offset=12)
design.add_deletion(helix=1, offset=24)
design.add_insertion(helix=0, offset=6, length=1)
design.add_insertion(helix=0, offset=18, length=2)
design.add_insertion(helix=1, offset=6, length=3)
design.add_insertion(helix=1, offset=18, length=4)
return design
def add_precursor_staples(design: sc.Design, staple_domain, label = None, dna_seq = None):
"""Add precursor staples to the design"""
for helix in range(len(staple_domain)):
if dna_seq == None:
seq = None
else:
seq = dna_seq[helix]
forward = sc_general.forward_strand(helix, 'staple')
outline = staple_domain[helix]
for i in range(outline[0] + 1):
lines = outline[1]
line = lines[i]
start = line[0]
end = line[1]
staples = sc.Strand([sc.Domain(helix = helix, forward = forward, start = start, end = end, label = label)], dna_sequence = seq)
design.add_strand(staples)
def add_precursor_scaffolds(design: sc.Design, shape_outline, label = None, dna_seq = None):
"""Adds the precursor scaffold to the design"""
for helix in range(len(shape_outline)):
if dna_seq == None:
seq = None
else:
seq = dna_seq[helix]
forward = sc_general.forward_strand(helix, 'scaffold')
one_line_outline = shape_outline[helix]
for i in range(one_line_outline[0] + 1):
lines = one_line_outline[1]
line = lines[i]
start = line[0]
end = line[1]
scaffold = sc.Strand([sc.Domain(helix = helix, forward = forward, start = start, end = end, label = label)], dna_sequence = seq, name = 'scaffold')
design.add_strand(scaffold)
def _create_left_edge_staples(offset_start: int, num_helices: int,
num_flanking_helices: int, idt: bool):
staples = []
crossover_right = offset_start + BASES_PER_COLUMN
for helix in range(0 + num_flanking_helices,
num_helices + num_flanking_helices, 2):
bot_helix_forward = True
ss_5p_bot = sc.Substrand(helix=helix + 1,
forward=bot_helix_forward,
start=offset_start,
end=crossover_right)
ss_3p_top = sc.Substrand(helix=helix,
forward=not bot_helix_forward,
start=offset_start,
end=crossover_right)
staple = sc.Strand(substrands=[ss_5p_bot, ss_3p_top])
staples.append(staple)
return staples
def _create_right_edge_staples(offset_end: int, num_helices: int,
num_flanking_helices: int) -> List[sc.Strand]:
staples = []
crossover_left = offset_end - BASES_PER_COLUMN
for helix in range(0 + num_flanking_helices,
num_helices + num_flanking_helices, 2):
bot_helix_forward = True
ss_5p_top = sc.Domain(helix=helix,
forward=not bot_helix_forward,
start=crossover_left,
end=offset_end)
ss_3p_bot = sc.Domain(helix=helix + 1,
forward=bot_helix_forward,
start=crossover_left,
end=offset_end)
staple = sc.Strand(domains=[ss_5p_top, ss_3p_bot])
staples.append(staple)
return staples
def create_design():
NUM_HELICES = 8
WIDTH = 16
doms = [sc.Domain(h, h % 2 == 0, 0, WIDTH) for h in range(NUM_HELICES)]
strand = sc.Strand(doms)
design = sc.Design(strands=[strand], grid=sc.square)
design.add_deletion(helix=0, offset=11)
design.add_deletion(helix=0, offset=12)
design.add_deletion(helix=1, offset=12)
design.add_insertion(helix=1, offset=4, length=1)
design.assign_dna(strand, 'T' * (NUM_HELICES * WIDTH))
strand.set_modification_5p(mod.biotin_5p)
strand.set_modification_3p(mod.cy3_3p)
for h in range(NUM_HELICES):
strand.set_modification_internal(WIDTH * h + 5, mod.cy3_int)
strand.set_modification_internal(WIDTH * h + 10, mod.biotin_int)
return design
def create_design() -> sc.Design:
ss_f0 = sc.Domain(helix=0, forward=True, start=0, end=8)
hairpin0 = sc.Loopout(length=5)
ss_r0 = sc.Domain(helix=0, forward=False, start=0, end=8)
crossover_like_loopout = sc.Loopout(length=5)
ss_f1 = sc.Domain(helix=1, forward=True, start=0, end=8)
long_range_loopout = sc.Loopout(length=10)
ss_r2 = sc.Domain(helix=2, forward=False, start=16, end=24)
hairpin2 = sc.Loopout(length=20)
ss_f2 = sc.Domain(helix=2, forward=True, start=16, end=32)
hairpin2_2 = sc.Loopout(length=1)
ss_r2_2 = sc.Domain(helix=2, forward=False, start=24, end=32)
strand = sc.Strand([
ss_f0, hairpin0, ss_r0, crossover_like_loopout, ss_f1,
long_range_loopout, ss_r2, hairpin2, ss_f2, hairpin2_2, ss_r2_2
])
design = sc.Design(strands=[strand], grid=sc.square)
t5 = 'TTTAC'
t10 = 'TTTACTTACG'
t20 = 'TTTTTTTTTTACGTTGCAGG'
design.assign_dna(
strand, f'ACGACGAC '
f'{t5} '
f'???????? '
f'{t5} '
f'GACGACGA '
f'{t10} '
f'CACGACGA '
f'{t20} '
f'???????? '
f'ACGACGAC '
f'T')
return design
def _create_scaffold(offset_start: int, offset_end: int, offset_mid: int, num_helices: int,
num_flanking_helices: int, scaffold_nick_offset: int):
# top domain is continguous
top_domain = sc.Domain(helix=0 + num_flanking_helices, forward=True,
start=offset_start, end=offset_end)
domains_left = []
domains_right = []
if scaffold_nick_offset < 0:
scaffold_nick_offset = offset_mid
for helix in range(1 + num_flanking_helices, num_helices + num_flanking_helices):
# otherwise there's a nick (bottom helix) or the seam crossover (all other than top and bottom)
# possibly nick on bottom helix is not along seam
center_offset = offset_mid if helix < num_helices + num_flanking_helices - 1 else scaffold_nick_offset
forward = (helix % 2 == num_flanking_helices % 2)
left_domain = sc.Domain(helix=helix, forward=forward,
start=offset_start, end=center_offset)
right_domain = sc.Domain(helix=helix, forward=forward,
start=center_offset, end=offset_end)
domains_left.append(left_domain)
domains_right.append(right_domain)
domains_left.reverse()
domains = domains_left + [top_domain] + domains_right
return sc.Strand(domains=domains, color=sc.default_scaffold_color, is_scaffold=True)
def initial_design():
max_offset = 1295
helices = [
# below uses cadnano honeycomb coordinates
# https://github.com/UC-Davis-molecular-computing/scadnano-python-package/blob/master/misc/cadnano-format-specs/v2.txt
sc.Helix(grid_position=(1, 1, 0), max_offset=max_offset),
sc.Helix(grid_position=(0, 1, 0), max_offset=max_offset),
sc.Helix(grid_position=(0, 2, 0), max_offset=max_offset),
sc.Helix(grid_position=(1, 2, 0), max_offset=max_offset),
sc.Helix(grid_position=(2, 2, 0), max_offset=max_offset),
sc.Helix(grid_position=(2, 1, 0), max_offset=max_offset),
# below uses original mistaken convention from mistaken cadnano specs
# sc.Helix(grid_position=(1, 0, 0), max_offset=max_offset),
# sc.Helix(grid_position=(0, 0, 0), max_offset=max_offset),
# sc.Helix(grid_position=(0, 1, 0), max_offset=max_offset),
# sc.Helix(grid_position=(1, 1, 0), max_offset=max_offset),
# sc.Helix(grid_position=(2, 1, 0), max_offset=max_offset),
# sc.Helix(grid_position=(2, 0, 0), max_offset=max_offset),
# # below uses odd-q coordinates:
# sc.Helix(grid_position=(1, -1, 0), max_offset=max_offset),
# sc.Helix(grid_position=(0, 0, 0), max_offset=max_offset),
# sc.Helix(grid_position=(0, 1, 0), max_offset=max_offset),
# sc.Helix(grid_position=(1, 1, 0), max_offset=max_offset),
# sc.Helix(grid_position=(2, 1, 0), max_offset=max_offset),
# sc.Helix(grid_position=(2, 0, 0), max_offset=max_offset),
# below uses even-q coordinates:
# sc.Helix(grid_position=(1, 0, 0), max_offset=max_offset),
# sc.Helix(grid_position=(0, 0, 0), max_offset=max_offset),
# sc.Helix(grid_position=(0, 1, 0), max_offset=max_offset),
# sc.Helix(grid_position=(1, 2, 0), max_offset=max_offset),
# sc.Helix(grid_position=(2, 1, 0), max_offset=max_offset),
# sc.Helix(grid_position=(2, 0, 0), max_offset=max_offset),
# below uses odd-r coordinates:
# sc.Helix(grid_position=(1, 0, 0), max_offset=max_offset),
# sc.Helix(grid_position=(0, 1, 0), max_offset=max_offset),
# sc.Helix(grid_position=(1, 2, 0), max_offset=max_offset),
# sc.Helix(grid_position=(2, 2, 0), max_offset=max_offset),
# sc.Helix(grid_position=(2, 1, 0), max_offset=max_offset),
# sc.Helix(grid_position=(2, 0, 0), max_offset=max_offset),
]
scafs = [
sc.Strand([sc.Domain(helix=0, forward=True, start=16, end=1276)]),
sc.Strand([sc.Domain(helix=1, forward=False, start=16, end=1276)]),
sc.Strand([sc.Domain(helix=2, forward=True, start=12, end=1272)]),
sc.Strand([sc.Domain(helix=3, forward=False, start=12, end=1272)]),
sc.Strand([sc.Domain(helix=4, forward=True, start=19, end=1279)]),
sc.Strand([sc.Domain(helix=5, forward=False, start=19, end=1279)]),
]
staps = [
sc.Strand([sc.Domain(helix=0, forward=False, start=42, end=1246)]),
sc.Strand([sc.Domain(helix=1, forward=True, start=42, end=1246)]),
sc.Strand([sc.Domain(helix=2, forward=False, start=42, end=1246)]),
sc.Strand([sc.Domain(helix=3, forward=True, start=42, end=1246)]),
sc.Strand([sc.Domain(helix=4, forward=False, start=42, end=1246)]),
sc.Strand([sc.Domain(helix=5, forward=True, start=42, end=1246)]),
]
strands = scafs + staps
return sc.DNADesign(helices=helices, strands=strands, grid=sc.honeycomb)
def add_precursor_staples(design: sc.Design):
staples = [sc.Strand([sc.Domain(helix=helix, forward=helix % 2 == 1, start=8, end=296)])
for helix in range(24)]
for staple in staples:
design.add_strand(staple)
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)
def main():
helices = [
sc.Helix(max_offset=64),
sc.Helix(max_offset=64),
sc.Helix(max_offset=64)
]
# left staple
stap_left_ss1 = sc.Domain(helix=1, forward=True, start=0, end=16)
stap_left_ss0 = sc.Domain(helix=0, forward=False, start=0, end=16)
stap_left = sc.Strand(domains=[stap_left_ss1, stap_left_ss0])
# right staple
stap_right_ss0 = sc.Domain(helix=0, forward=False, start=16, end=32)
stap_right_ss1 = sc.Domain(helix=1, forward=True, start=16, end=32)
stap_right = sc.Strand(domains=[stap_right_ss0, stap_right_ss1])
# scaffold
scaf_ss1_left = sc.Domain(helix=1, forward=False, start=0, end=16)
scaf_ss0 = sc.Domain(helix=0, forward=True, start=0, end=32)
loopout = sc.Loopout(length=3)
scaf_ss1_right = sc.Domain(helix=1, forward=False, start=16, end=32)
scaf = sc.Strand(
domains=[scaf_ss1_left, scaf_ss0, loopout, scaf_ss1_right],
is_scaffold=True)
ss_extra1 = sc.Domain(helix=1, forward=True, start=32, end=48)
ss_extra2 = sc.Domain(helix=1, forward=True, start=48, end=64)
ss_extra3 = sc.Domain(helix=2, forward=False, start=32, end=48)
ss_extra1b = sc.Domain(helix=1, forward=False, start=32, end=48)
ss_extra2b = sc.Domain(helix=1, forward=False, start=48, end=64)
ss_extra3b = sc.Domain(helix=2, forward=True, start=32, end=48)
ss_extra4 = sc.Domain(helix=2, forward=True, start=16, end=32)
ss_extra5 = sc.Domain(helix=2, forward=True, start=0, end=16)
s_extra1 = sc.Strand(domains=[ss_extra1])
s_extra2 = sc.Strand(domains=[ss_extra2])
s_extra3 = sc.Strand(domains=[ss_extra3])
s_extra4 = sc.Strand(domains=[ss_extra4])
s_extra5 = sc.Strand(domains=[ss_extra5])
s_extra1b = sc.Strand(domains=[ss_extra1b])
s_extra2b = sc.Strand(domains=[ss_extra2b])
s_extra3b = sc.Strand(domains=[ss_extra3b])
# whole design
design = sc.DNADesign(helices=helices,
strands=[
scaf, stap_left, stap_right, s_extra1, s_extra2,
s_extra3, s_extra4, s_extra1b, s_extra2b,
s_extra3b, s_extra5
],
grid=sc.square)
# deletions and insertions added to design so they can be added to both strands on a helix
design.add_deletion(helix=0, offset=11)
design.add_deletion(helix=0, offset=12)
design.add_deletion(helix=0, offset=24)
design.add_deletion(helix=1, offset=12)
design.add_deletion(helix=1, offset=24)
design.add_insertion(helix=0, offset=6, length=1)
design.add_insertion(helix=0, offset=18, length=2)
design.add_insertion(helix=1, offset=6, length=3)
design.add_insertion(helix=1, offset=18, length=4)
# DNA assigned to whole design so complement can be assigned to strands other than scaf
design.assign_dna(scaf, 'AACT' * 18)
design.assign_dna(s_extra1, 'AACT' * 4)
design.assign_dna(s_extra2, 'GGTA' * 4)
return design
def _create_inner_staples(offset_start: int, offset_end: int, offset_mid: int,
num_helices: int, num_flanking_helices: int,
num_cols: int,
nick_pattern: NickPattern) -> List[sc.Strand]:
if nick_pattern is not NickPattern.staggered:
raise NotImplementedError(
"Currently can only handle staggered nick pattern")
# if ((num_cols - 4) // 2) % 2 != 0:
# raise NotImplementedError("Currently can only handle num_cols such that an even number of "
# "columns appear between each edge column and seam column, "
# "i.e., ((num_cols - 4) // 2) % 2 == 0")
len_half_col = BASES_PER_COLUMN // 2
staples = []
for col in range(num_cols):
x_l = offset_start + BASES_PER_COLUMN * col
x_r = offset_start + BASES_PER_COLUMN * (col + 1)
x_mid_col = x_l + len_half_col
if (x_l == offset_start # skip left edge column
or x_r == offset_mid # skip left seam column
or x_l == offset_mid # skip right seam column
or x_r == offset_end): # skip right edge column
continue
if col % 2 == 1:
# special staple in odd column is 24-base staple along top helix
h1_forward = True
ss_top_5p_h0 = sc.Domain(helix=0 + num_flanking_helices,
forward=not h1_forward,
start=x_l,
end=x_mid_col + BASES_PER_COLUMN)
ss_top_3p_h1 = sc.Domain(helix=1 + num_flanking_helices,
forward=h1_forward,
start=x_l,
end=x_mid_col)
staple_top = sc.Strand(domains=[ss_top_5p_h0, ss_top_3p_h1])
staples.append(staple_top)
for helix in range(1 + num_flanking_helices,
num_helices + num_flanking_helices - 2, 2):
helix_i_forward = True
ss_helix_i = sc.Domain(helix=helix,
forward=helix_i_forward,
start=x_mid_col,
end=x_r)
ss_helix_ip1 = sc.Domain(helix=helix + 1,
forward=not helix_i_forward,
start=x_l,
end=x_r)
ss_helix_ip2 = sc.Domain(helix=helix + 2,
forward=helix_i_forward,
start=x_l,
end=x_mid_col)
staple = sc.Strand(
domains=[ss_helix_i, ss_helix_ip1, ss_helix_ip2])
staples.append(staple)
else:
# special staple in even column is 24-base staple along bottom helix (hm1="helix minus 1")
hm1_forward = True
ss_bot_5p_hm1 = sc.Domain(helix=num_helices +
num_flanking_helices - 1,
forward=hm1_forward,
start=x_mid_col - BASES_PER_COLUMN,
end=x_r)
ss_bot_3p_hm2 = sc.Domain(helix=num_helices +
num_flanking_helices - 2,
forward=not hm1_forward,
start=x_mid_col,
end=x_r)
staple_bot = sc.Strand(domains=[ss_bot_5p_hm1, ss_bot_3p_hm2])
staples.append(staple_bot)
for helix in range(0 + num_flanking_helices,
num_helices + num_flanking_helices - 3, 2):
helix_i_forward = False
ss_helix_i = sc.Domain(helix=helix,
forward=helix_i_forward,
start=x_mid_col,
end=x_r)
ss_helix_ip1 = sc.Domain(helix=helix + 1,
forward=not helix_i_forward,
start=x_l,
end=x_r)
ss_helix_ip2 = sc.Domain(helix=helix + 2,
forward=helix_i_forward,
start=x_l,
end=x_mid_col)
staple = sc.Strand(
domains=[ss_helix_ip2, ss_helix_ip1, ss_helix_i])
staples.append(staple)
return staples
def precursor_scaffolds() -> sc.Design:
helices = [sc.Helix(max_offset=304) for _ in range(24)]
scaffolds = [sc.Strand([sc.Domain(helix=helix, forward=helix % 2 == 0, start=8, end=296)])
for helix in range(24)]
return sc.Design(helices=helices, strands=scaffolds, grid=sc.square)
