def precursor_staples(design: sc.Design):
#2D design has to be topologically a circle
# helices = [sc.Helix(max_offset=int(block*cmax)) for _ in range(maxhelix)]
staples = []
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
staples.append(
sc.Strand([
sc.Domain(helix=2 * helix,
forward=((2 * helix) % 2 == 1),
start=start,
end=end)
]))
staples.append(
sc.Strand([
sc.Domain(helix=(2 * helix) + 1,
forward=((2 * helix + 1) % 2 == 1),
start=start,
end=end)
]))
for staple in staples:
design.add_strand(staple)
def add_staple_precursors(design: sc.Design) -> None:
staples = [
sc.Strand(
[sc.Domain(helix=helix, forward=helix % 2 == 1, start=0,
end=288)]) # noqa
for helix in range(24)
]
for staple in staples:
design.add_strand(staple)
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 add_tiles_and_assign_dna(design: sc.Design) -> None:
# left tiles
left_left = 11
left_right = 32
for top_helix, seq in zip(range(2, 18, 2), tile_dna_seqs):
bot_helix = top_helix + 1
ss_top = sc.Domain(helix=top_helix,
forward=True,
start=left_left,
end=left_right)
ss_bot = sc.Domain(helix=bot_helix,
forward=False,
start=left_left,
end=left_right)
idt = sc.IDTFields(name=f'tile-left-{top_helix}-{bot_helix}',
scale='25nm',
purification='STD')
tile = sc.Strand(domains=[ss_bot, ss_top],
color=sc.Color(0, 0, 0),
idt=idt)
design.add_strand(tile)
design.assign_dna(tile, seq)
# right tiles
right_left = 480
right_right = 501
for top_helix, seq in zip(range(2, 18, 2), tile_dna_seqs):
bot_helix = top_helix + 1
ss_top = sc.Domain(helix=top_helix,
forward=True,
start=right_left,
end=right_right)
ss_bot = sc.Domain(helix=bot_helix,
forward=False,
start=right_left,
end=right_right)
idt = sc.IDTFields(name=f'tile-right-{top_helix}-{bot_helix}',
scale='25nm',
purification='STD')
tile = sc.Strand(domains=[ss_bot, ss_top],
color=sc.Color(0, 0, 0),
idt=idt)
design.add_strand(tile)
design.assign_dna(tile, seq)
def add_adapters(design: sc.Design) -> None:
# 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 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)
