def main():
length = 16
helices = [
sc.Helix(major_tick_distance=4,
max_offset=length,
position=sc.Position3D(x=0, y=0, z=0),
min_offset=0),
sc.Helix(major_tick_distance=4,
max_offset=length,
position=sc.Position3D(x=0, y=3, z=3),
min_offset=8),
sc.Helix(major_tick_distance=4,
max_offset=length,
position=sc.Position3D(x=2.5, y=-3, z=8),
min_offset=0),
sc.Helix(major_tick_distance=4,
max_offset=length,
position=sc.Position3D(x=2.5, y=1, z=11),
min_offset=8),
]
design = sc.DNADesign(helices=helices,
strands=[
sc.Strand([sc.Domain(0, True, 0, length)]),
sc.Strand([sc.Domain(1, True, 8, length)]),
sc.Strand([sc.Domain(2, True, 0, length)]),
sc.Strand([sc.Domain(3, True, 8, length)]),
],
grid=sc.Grid.none)
return design
def main():
# 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])
stap_right.set_modification_5p(mod.biotin_5p)
# 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.DNADesign(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 create_design():
length = 10
helices = [
sc.Helix(max_offset=length,
position=sc.Position3D(x=0, y=0, z=2.5),
pitch=0,
roll=0,
yaw=0),
sc.Helix(max_offset=length,
position=sc.Position3D(x=3, y=3, z=0),
pitch=0,
roll=0,
yaw=0),
sc.Helix(max_offset=length,
position=sc.Position3D(x=8, y=-3, z=0),
pitch=0,
roll=0,
yaw=0),
sc.Helix(max_offset=length,
position=sc.Position3D(x=11, y=1, z=0),
pitch=0,
roll=0,
yaw=0),
]
stap_ss = sc.Domain(0, True, 0, length)
scaf_ss = sc.Domain(0, False, 0, length)
stap = sc.Strand([stap_ss])
scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
strands = [stap, scaf]
design = sc.Design(helices=helices, strands=strands, grid=sc.Grid.none)
return design
def main():
helices = [
sc.Helix(idx=2, max_offset=20),
sc.Helix(idx=3, max_offset=20),
sc.Helix(idx=5, max_offset=20),
sc.Helix(idx=7, max_offset=20),
sc.Helix(idx=11, max_offset=20),
]
design = sc.DNADesign(helices=helices, strands=[])
# design.set_helices_view_order([5, 2, 11, 3, 7])
return design
def main():
num_helices = 16
bases = 48
helices = [sc.Helix() for _ in range(num_helices)]
strands = []
for bot in range(num_helices // 2):
top = num_helices - bot - 1
helix_top = helices[bot]
helix_bot = helices[top]
stap_left_ss_top = sc.Domain(top, sc.forward, 0, bases // 3)
stap_left_ss_bot = sc.Domain(bot, sc.reverse, 0, bases // 3)
stap_mid_ss_bot = sc.Domain(bot, sc.reverse, bases // 3,
bases * 2 // 3)
stap_mid_ss_top = sc.Domain(top, sc.forward, bases // 3,
bases * 2 // 3)
stap_right_ss_top = sc.Domain(top, sc.forward, bases * 2 // 3, bases)
stap_right_ss_bot = sc.Domain(bot, sc.reverse, bases * 2 // 3, bases)
stap_left = sc.Strand([stap_left_ss_bot, stap_left_ss_top])
stap_mid = sc.Strand([stap_mid_ss_top, stap_mid_ss_bot])
stap_right = sc.Strand([stap_right_ss_bot, stap_right_ss_top])
strands.append(stap_left)
strands.append(stap_mid)
strands.append(stap_right)
design = sc.DNADesign(helices=helices, strands=strands, grid=sc.square)
return design
def main():
length = 16
helices = [sc.Helix(max_offset=length, grid_position=(h, v, 0))
for v in range(-4, 6) for h in range(-4, 6)]
design = sc.DNADesign(helices=helices, strands=[], grid=sc.hexagonal)
return design
def precursor_scaffolds() -> sc.Design:
#2D design has to be topologically a circle
helices = [sc.Helix(max_offset=int(block * cmax)) for _ in range(maxhelix)]
scaffolds = []
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
scaffolds.append(
sc.Strand([
sc.Domain(helix=2 * helix,
forward=((2 * helix) % 2 == 0),
start=start,
end=end)
]))
scaffolds.append(
sc.Strand([
sc.Domain(helix=(2 * helix) + 1,
forward=((2 * helix + 1) % 2 == 0),
start=start,
end=end)
]))
return sc.Design(helices=helices, strands=scaffolds, grid=sc.square)
def main():
helices = [sc.Helix(0, 25), sc.Helix(1, 25)]
s1_left_ss0 = sc.Domain(0, sc.reverse, 0, 5)
s1_ss1 = sc.Domain(0, sc.forward, 0, 15)
s1_right_ss0 = sc.Domain(0, sc.reverse, 5, 15)
s1 = sc.Strand([s1_left_ss0, s1_ss1, s1_right_ss0])
s2_ss1 = sc.Domain(0, sc.forward, 10, 20)
s2_ss0 = sc.Domain(0, sc.reverse, 10, 20)
s2 = sc.Strand([s2_ss1, s2_ss0])
strands = [s1, s2]
design = sc.Design(helices=helices, strands=strands, grid=sc.square)
return design
def create_design() -> sc.Design:
length = 16
helices = [sc.Helix(max_offset=length, grid_position=(h, v))
for v in range(-4, 6) for h in range(-4, 6)]
design = sc.Design(helices=helices, strands=[], grid=sc.honeycomb)
return design
def create_design():
length = 30
helices = [
sc.Helix(min_offset=0, max_offset=length, grid_position=(0, 0)),
sc.Helix(min_offset=1, max_offset=length, grid_position=(0, 1)),
sc.Helix(min_offset=2, max_offset=length, grid_position=(0, 2)),
sc.Helix(min_offset=3, max_offset=length, grid_position=(0, 3)),
]
stap_ss = sc.Domain(0, True, 0, length - 1)
scaf_ss = sc.Domain(0, False, 0, length - 1)
stap = sc.Strand([stap_ss])
scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
strands = [stap, scaf]
design = sc.Design(helices=helices, strands=strands, grid=sc.Grid.square)
return design
def create_design() -> sc.Design:
blue = sc.Color(r=0, g=0, b=255)
black = sc.Color(r=0, g=0, b=0)
red = sc.Color(r=255, g=0, b=0)
green = sc.Color(r=0, g=150, b=0)
cols = 8
rows = 8
helices = [sc.Helix(major_tick_distance=10) for _ in range(rows + 1)]
strands = []
for col in range(cols):
for row in range(rows):
helix = row
forward = row % 2 == 0
if forward:
offset = col * 20
ss1 = sc.Domain(helix, forward, offset, offset + 20)
ss2 = sc.Domain(helix + 1, forward, offset + 20, offset + 40)
else:
offset = col * 20
ss2 = sc.Domain(helix, forward, offset + 10, offset + 30)
ss1 = sc.Domain(helix + 1, forward, offset + 30, offset + 50)
if forward:
color = blue if col % 2 == 0 else black
else:
color = red if col % 2 == 0 else green
strand = sc.Strand([ss1, ss2], color=color)
strands.append(strand)
design = sc.Design(helices=helices, strands=strands, grid=sc.square)
return design
def create_design() -> sc.Design:
helices = []
num_helices, max_bases = 30, 2000
for _ in range(num_helices):
helices.append(sc.Helix(max_bases))
design = sc.Design(helices=helices, strands=[], grid=sc.square)
return design
def precursor_scaffolds() -> sc.DNADesign:
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.DNADesign(helices=helices, strands=scaffolds, grid=sc.square)
def create_design() -> sc.Design:
helices = [sc.Helix(max_offset=24) for _ in range(2)]
design = sc.Design(helices=helices, grid=sc.square)
design.strand(0, 0).move(8).cross(1).move(-8).as_circular()
design.strand(0, 8).move(8).loopout(1, 5).move(-8).as_circular()
design.strand(0, 16).move(8).cross(1).move(-8)
return design
def create_design():
length = 16
helices = [
sc.Helix(max_offset=length, grid_position=(h, v)) for v in range(10)
for h in range(10)
]
design = sc.Design(helices=helices, strands=[], grid=sc.hexagonal)
return design
def main():
# 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)
# geometry
geometry = sc.Geometry(rise_per_base_pair=0.2,
helix_radius=1.2,
inter_helix_gap=1.0)
# whole design
design = sc.DNADesign(helices=helices,
strands=[scaf, stap_left, stap_right],
grid=sc.square,
geometry=geometry)
# 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 create_design() -> sc.Design:
# helices
helices = [sc.Helix(max_offset=48), sc.Helix(max_offset=48)]
# whole design
design = sc.Design(helices=helices, strands=[], grid=sc.square)
design.strand(1, 8).to(24).cross(0).to(8) # left staple
design.strand(0, 40).to(24).cross(1).to(40).with_modification_5p(mod.biotin_5p) # right staple
design.strand(1, 24).to(8).cross(0).to(40).loopout(1, 3).to(24).as_scaffold()
# 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(design.scaffold, 'AACGT' * 18)
return design
def create_design() -> sc.Design:
length = 9
helices = [sc.Helix(max_offset=length, roll=90)]
stap_ss = sc.Domain(0, True, 0, length)
scaf_ss = sc.Domain(0, False, 0, length)
stap = sc.Strand([stap_ss])
scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
strands = [stap, scaf]
design = sc.Design(helices=helices, strands=strands, grid=sc.square)
design.assign_dna(scaf, 'AACT' * (length // 4))
return design
def main():
length = 9
helices = [sc.Helix(max_offset=length, major_ticks=[2, 5])]
stap_ss = sc.Domain(0, True, 0, length)
scaf_ss = sc.Domain(0, False, 0, length)
stap = sc.Strand([stap_ss])
scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
strands = [stap, scaf]
design = sc.DNADesign(helices=helices, strands=strands, grid=sc.square)
design.assign_dna(scaf, 'AACT' * (length // 4))
return design
def main():
length = 9
helices = [sc.Helix(max_offset=length, rotation=math.pi/2, rotation_anchor=2)]
stap_ss = sc.Domain(0, sc.forward, 0, length)
scaf_ss = sc.Domain(0, sc.reverse, 0, length)
stap = sc.Strand([stap_ss])
scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
strands = [stap, scaf]
design = sc.DNADesign(helices=helices, strands=strands, grid=sc.square)
design.assign_dna(scaf, 'AACT' * (length // 4))
return design
def initial_design() -> sc.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), max_offset=max_offset),
sc.Helix(grid_position=(0, 1), max_offset=max_offset),
sc.Helix(grid_position=(0, 2), max_offset=max_offset),
sc.Helix(grid_position=(1, 2), max_offset=max_offset),
sc.Helix(grid_position=(2, 2), max_offset=max_offset),
sc.Helix(grid_position=(2, 1), 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.Design(helices=helices, strands=strands, grid=sc.honeycomb)
def create_design() -> sc.Design:
helices = [sc.Helix(max_offset=288) for _ in range(24)]
design = sc.Design(helices=helices, grid=sc.square)
add_scaffold_precursors(design)
add_scaffold_crossovers(design)
add_staple_precursors(design)
add_staple_crossovers(design)
add_staple_nicks(design)
add_twist_correction_deletions(design)
design.assign_m13_to_scaffold()
return design
def create_design():
length = 9
helices = [
sc.Helix(max_offset=length,
major_ticks=[2, 5],
position=sc.Position3D(x=1, y=2, z=3),
pitch=90)
]
stap_ss = sc.Domain(0, True, 0, length)
scaf_ss = sc.Domain(0, False, 0, length)
stap = sc.Strand([stap_ss])
scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
strands = [stap, scaf]
design = sc.Design(helices=helices, strands=strands, grid=sc.Grid.none)
design.assign_dna(scaf, 'AACT' * (length // 4))
return design
def main():
length = 9
helices = [
sc.Helix(max_offset=length,
major_ticks=[2, 5],
position3d=sc.Position3D(x=3, y=2, z=1),
pitch=90)
]
stap_ss = sc.Domain(0, sc.forward, 0, length)
scaf_ss = sc.Domain(0, sc.reverse, 0, length)
stap = sc.Strand([stap_ss])
scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
strands = [stap, scaf]
design = sc.DNADesign(helices=helices, strands=strands, grid=sc.square)
design.assign_dna(scaf, 'AACT' * (length // 4))
return design
def create_helices(shape_outline, lattice, hex_or_square) -> sc.Design:
"""Given the outline, complete lattice, and if the lattice is hex or square, creates the base helices without any strands"""
if hex_or_square == 'hex':
grid_type = sc.hexagonal
elif hex_or_square == 'square':
grid_type = sc.square
else:
raise Exception("Error in create_helices(), input for hex_or_square must be eihter 'hex' or 'square'")
max_offset = sc_general.find_max(shape_outline)
size = len(lattice)
helices = []
for i in range(size):
position = lattice[i]
helices.append(sc.Helix(max_offset = max_offset, grid_position = position))
design = sc.Design(helices = helices, strands = [], grid = grid_type)
return design
def create_design() -> sc.Design:
num_domains = 9
helices = [sc.Helix(max_offset=(num_domains) * 8)]
design: sc.Design = sc.Design(helices=helices, strands=[], grid=sc.square)
design.strand(0, (num_domains - 1) * 8) \
.move(-8).with_domain_name('domain 8*') \
.move(-8).with_domain_name('domain 7*') \
.move(-8).with_domain_name('domain 6*') \
.move(-8).with_domain_name('domain 5*') \
.move(-8).with_domain_name('domain 4*') \
.move(-8).with_domain_name('domain 3*') \
.move(-8).with_domain_name('domain 2*') \
.move(-8).with_domain_name('domain 1*') \
.with_name('bottom strand')
# domain names match
design.strand(
0, 0).move(8).with_domain_name('domain 1').with_name('top strand 1')
# domains are aligns but names mismatch
design.strand(
0, 8).move(8).with_domain_name('domain 50').with_name('top strand 2')
# domain names match
design.strand(
0, 16).move(8).with_domain_name('domain 3').with_name('top strand 3')
# domain names are the same, not complementary
design.strand(
0, 24).move(8).with_domain_name('domain 4*').with_name('top strand 4')
# domain names match but domains are mis-aligned
design.strand(
0, 32).move(9).with_domain_name('domain 5').with_name('top strand 5')
# domain names match but domains are mis-aligned
design.strand(
0, 48).move(7).with_domain_name('domain 7').with_name('top strand 7')
# no overlap so no mismatch
design.strand(
0, 64).move(8).with_domain_name('domain 9').with_name('top strand 9')
return design
def _create_helices(num_helices: int,
num_bases_per_helix: int) -> List[sc.Helix]:
return [
sc.Helix(max_offset=num_bases_per_helix) for _ in range(num_helices)
]
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_helices(num_helices: int, num_bases_per_helix: int):
return [
sc.Helix(max_bases=num_bases_per_helix) for _ in range(num_helices)
]
def create_design():
include_rot = False
include_rot = True
n = 'north'
e = 'east'
s = 'south'
w = 'west'
helices = [
sc.Helix(max_offset=20, group=n, grid_position=(0, 0)), # 0
sc.Helix(max_offset=21, group=n, grid_position=(1, 0)), # 1
sc.Helix(max_offset=19, group=n, grid_position=(1, 1)), # 2
sc.Helix(max_offset=18, group=n, grid_position=(0, 1)), # 3
sc.Helix(max_offset=17, group=n, grid_position=(-1, 1)), # 4
sc.Helix(max_offset=16, group=n, grid_position=(-1, 0)), # 5
sc.Helix(max_offset=24, group=s), # 6
sc.Helix(max_offset=25, group=s), # 7
sc.Helix(max_offset=26, group=w, position=sc.Position3D(x=0, y=0,
z=0)), # 8
sc.Helix(max_offset=27, group=w, position=sc.Position3D(x=0, y=3,
z=0)), # 9
]
if include_rot:
helices.extend([
sc.Helix(max_offset=26, group='r', grid_position=(0, 0)), # 10
sc.Helix(max_offset=27, group='r', grid_position=(0, 1)), # 11
])
helices.extend([
sc.Helix(idx=13, max_offset=22, group=e), # 13
sc.Helix(idx=15, max_offset=23, group=e), # 15
])
group_north = sc.HelixGroup(position=sc.Position3D(x=0, y=-10, z=0),
grid=sc.honeycomb)
group_south = sc.HelixGroup(position=sc.Position3D(x=0, y=10, z=0),
helices_view_order=[7, 6],
grid=sc.square)
group_east = sc.HelixGroup(position=sc.Position3D(x=0, y=0, z=10),
grid=sc.square)
group_west = sc.HelixGroup(position=sc.Position3D(x=0, y=0, z=-10),
grid=sc.Grid.none)
groups = {
n: group_north,
e: group_east,
s: group_south,
w: group_west,
}
if include_rot:
group_rot = sc.HelixGroup(position=sc.Position3D(x=00, y=10, z=10),
pitch=45,
grid=sc.square)
groups['r'] = group_rot
design = sc.Design(helices=helices, groups=groups, strands=[])
design.strand(0, 0).to(8) \
.cross(1).to(0) \
.cross(2).to(8) \
.cross(3).to(0) \
.cross(4).to(8) \
.cross(5).to(0)
design.strand(4, 10).to(13)
design.strand(6, 0).to(8).cross(7).to(0)
design.strand(8, 0).to(8).cross(9).to(0)
design.strand(13, 0).to(8).cross(15).to(0)
design.strand(8, 8).to(11)
design.strand(13, 8).to(11)
if include_rot:
design.strand(10, 0).to(8).cross(11).to(0)
return design
