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():
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 idx_to_position(idx: int):
x = 0
y = 0
angle = 0
for _ in range(idx):
x += math.cos(angle) * 2.5
y += math.sin(angle) * 2.5
angle += 2 * math.pi / 16
return sc.Position3D(x=x, y=y)
def idx_to_position(idx: int) -> sc.Position3D:
z = 0
y = 0
angle = 0
for _ in range(idx):
z += math.cos(angle) * 2.5
y += math.sin(angle) * 2.5
angle += 2 * math.pi / 16
return sc.Position3D(x=0, y=y, z=z)
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_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 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