def long_route() -> LatticeRoute:
nodes = [
LatticeNode(np.array([0., 0., 10.])),
LatticeNode(np.array([0, 20. * 0.42, 10.]))
]
route = LatticeRoute(nodes)
return route
def test_route():
nodes = [
LatticeNode(np.array([0., 10., 0.])),
LatticeNode(np.array([0., 30., 0.])),
LatticeNode(np.array([30., 30., 0.])),
LatticeNode(np.array([30., 10., 0.])),
]
route = LatticeRoute(nodes)
assert len(route.edges) == 3
system = System(np.array([50., 50., 50.]))
system.add_strand(route)
assert len(system.strands) == 1
system = route.system(box=np.array([50., 50., 50.]))
assert len(system.strands) == 1
system.write_oxDNA(root=ROOT)
return route
def test_StapleRoute(route: LatticeRoute):
x1 = 0
x2 = 15
row = 0
scaffold_rows = route.get_strand()[1]
staple_nodes = [
StapleNode([x1, row, 0.0]),
StapleNode([x2, row, 0.0]),
StapleNode([x2, row + 1, 0.0]),
StapleNode([x1, row + 1, 0.0])
]
return StapleRoute(scaffold_rows, staple_nodes)
def route(self, crossovers=None, *args, **kwargs) -> List[LatticeNode]:
"""
Generate DNASnake scaffold route, returns list of LatticeNode objects
Arguments:
crossovers - binary array or list of coordinates of crossovers
*args & **kwargs - correspond to those of the `LatticeRoute` class
Note:
Different subclasses will use `Lattice` in a different way.
Moreover, they will probably have a different routing algorithm
"""
if crossovers is None:
coords = self.crossover_coords
elif np.shape(crossovers)[1] not in [2, 3]: # if array
coords = self.array_to_coords(crossovers)
else:
coords = crossovers
# add 3rd column (z = 0)
shape = np.shape(coords)
if shape[1] != 3:
coords = np.c_[coords, np.zeros(shape[0])]
crossovers_per_row = 2
lattice_rows = int(coords[:, 1].max() + 1) # coords counts from 0
vertices_in_route = int(crossovers_per_row * lattice_rows)
vertex_list = np.zeros((vertices_in_route, 3))
# Find final crossover from left or right and make it a node
for row in range(0, lattice_rows):
vertex_index_L = bisect_left(coords[:, 1], row)
vertex_index_R = bisect_right(coords[:, 1], row) - 1
if row % 2 == 0: # if even
vertex_list[row * 2] = coords[vertex_index_L]
vertex_list[row * 2 + 1] = coords[vertex_index_R]
else: # if odd
vertex_list[row * 2] = coords[vertex_index_R]
vertex_list[row * 2 + 1] = coords[vertex_index_L]
# print(vertex_list)
node_list = [LatticeNode(i) for i in vertex_list]
return LatticeRoute(node_list, *args, **kwargs)
def side_staples(route: LatticeRoute, staple_width=16):
scaffold = ScaffoldRows(route)
staples = []
scaffold_rows = route.get_strand()[1]
for row, info in scaffold.info.iterrows():
x2 = info["bounds"][0]
if info["start side"] == "left":
x1 = x2 + staple_width
elif info["start side"] == "right":
x1 = x2 - staple_width
staple_nodes = [
StapleNode([x1, row, 0.0]),
StapleNode([x2, row, 0.0]),
StapleNode([x2, row + 1, 0.0]),
StapleNode([x1, row + 1, 0.0])
]
staples.append(StapleRoute(scaffold_rows, staple_nodes))
return StapleCollection(staples)
return StapleRoute(scaffold_rows, staple_nodes)
if __name__ == "__main__":
half_turn_indices = [4, 15, 25, 36, 46, 56, 67, 77, 88, 98, 109]
staple_lengths = [9, 31, 51, 73]
route_vertices = [[0., 0., 0.], [56., 0., 0.], [56., 1., 0.], [0., 1., 0.],
[0., 2., 0.], [56., 2., 0.], [56., 3., 0.], [0., 3., 0.],
[0., 4., 0.], [56., 4., 0.], [56., 5., 0.], [0., 5., 0.],
[0., 6., 0.], [56., 6., 0.], [56., 7., 0.], [0., 7., 0.],
[0., 8., 0.], [88., 8., 0.], [88., 9., 0.], [0., 9., 0.],
[0., 10., 0.], [88., 10., 0.], [88., 11., 0.],
[0., 11., 0.], [0., 12., 0.], [56., 12., 0.],
[56., 13., 0.], [0., 13., 0.], [0., 14., 0.],
[56., 14., 0.], [56, 15, 0], [0, 15, 0]]
nodes = [LatticeNode(np.array(i)) for i in route_vertices]
route = LatticeRoute(nodes)
fig, ax = plt.subplots()
route.plot(ax=ax)
# test, scaf = test_StapleRoute(route)
# system = System(np.array([50,50,50]))
# system.add_strands(scaf)
# system.write_oxDNA("scaffold")
collection = side_staples(route)
system = route.system(collection.staples)
system.write_oxDNA("lol")