def generate(polygon_vertices: np.ndarray,
title: str = "polygon_name",
DNAout: bool = False,
PLOTout: bool = False):
print(f"{title}: Making polygon...")
polygon = BoundaryPolygon(polygon_vertices)
print(f"{title}: ...constructing scaffolding lattice...")
lattice = polygon.dna_snake(straightening_factor=5,
start_side="left",
grid_size=[0.34, 2.5])
print(f"{title}: ...calculating route.")
route = lattice.route()
if PLOTout:
print(f"{title}: Generating and saving lattice plot.")
plot_list = [lattice.quantised_array, lattice.crossover_coords]
lattice.plot(plot_list,
poly=True,
fout=title,
root=ROOT + "/lattice-plot_out/",
aspect=6)
route.plot()
if DNAout:
system = route.system()
print(f"{title}: Generating and saving oxDNA files.")
system.write_oxDNA(prefix=title, root=ROOT + "/oxDNA_out/")
print(f"{title}: Generating and saving LAMMPS files.")
system.write_LAMMPS(prefix=title, root=ROOT + "/LAMMPS_out/")
def generate(polygon_vertices: np.ndarray,
DNAout: str = None,
PLOTout: str = None):
polygon = BoundaryPolygon(polygon_vertices)
lattice = polygon.dna_snake(straightening_factor=5, start_side="left")
route = lattice.route()
if PLOTout:
plot_list = [lattice.quantised_array, lattice.crossover_coords]
lattice.plot(plot_list, poly=True)
route.plot()
def test_BoundaryPolygon():
square = BoundaryPolygon(
np.array([
[1, 0, 0],
[1, 1, 0],
[0, 1, 0],
[0, 0, 0],
]))
assert square.n_edges == len(square.edges)
assert square.x.sum() == 2
assert square.y.sum() == 2
assert square.z.sum() == 0
assert isinstance(square.edges[0], Edge)
# square.plot2D(show=False)
# square.write_STL(f"{ROOT}/square.stl")
square.write_PLY(f"{ROOT}/square.ply")
def main():
# read file
mesh = meshio.read("/home/shanil/drawNA/polygons/STL/hexagon.stl")
# output vertices
mesh = mesh.points
# use only vertices on the z = 0 plane
mesh = mesh[mesh[:, 2] == 0]
mesh = np.random.permutation(np.array(mesh))
permutations = itertools.permutations(range(0, mesh.shape[0]))
SHAPE = BoundaryPolygon(mesh)
SHAPE2 = SHAPE
SHAPE2 = np.vstack((SHAPE.vertices, SHAPE.vertices))
# make_polygon(mesh)
print(f"mesh shape is {mesh.shape[0]} \n and SHAPE2 is {SHAPE2}")
def shapeIsSimple(SHAPE3):
# make_polygon(SHAPE3)
return LineString(SHAPE3).is_simple
perm = next(permutations)
for j in range(0, math.factorial(mesh.shape[0])):
SHAPE3 = SHAPE2[perm[0]]
for i in range(1, mesh.shape[0]):
SHAPE3 = np.vstack((SHAPE3, SHAPE2[perm[i]]))
if shapeIsSimple(SHAPE3): # no intersections
print(f"Finally \n Updated orientation: {SHAPE3}")
break
perm = next(permutations)
print(f"Permutation: {perm}")
make_polygon(SHAPE3)
import numpy as np
from drawNA.polygons import BoundaryPolygon, make_polygon
###---stored arrays of some shapes---###
square = np.array([[0, 0, 0], [0.0, 1.0, 0.0], [1.0, 1.0, 0.0],
[1.0, 0.0, 0.0]])
trapezium = np.array([[0, 0, 0], [1.0, 10.0, 0.0], [11.0, 10.0, 0.0],
[15.0, 0.0, 0.0]])
no = 0.866025
hexagon = np.array([[0, 1, 0], [no, 0.5, 0], [no, -0.5, 0], [0, -1, 0],
[-no, -0.5, 0], [-no, 0.5, 0]])
star = np.array([
[0, 300, 0],
[100, 110, 0],
[300, 70, 0],
[160, -90, 0],
[190, -300, 0],
[0, -210, 0],
[-190, -300, 0],
[-160, -90, 0],
[-300, 70, 0],
[-100, 110, 0],
])
###---run the program---###
SHAPE = BoundaryPolygon(star)
make_polygon(star, SHAPE)
###---stored arrays of some shapes---###
square = np.array([[0, 0, 0], [0.0, 1.0, 0.0], [1.0, 1.0, 0.0], [1.0, 0.0, 0.0]])
trapezium = np.array([[0, 0, 0], [1.0, 10.0, 0.0], [11.0, 10.0, 0.0], [15.0, 0.0, 0.0]])
no = 0.866025
hexagon = np.array(
[[0, 1, 0], [no, 0.5, 0], [no, -0.5, 0], [0, -1, 0], [-no, -0.5, 0], [-no, 0.5, 0]]
)
star = np.array(
[
[0, 300, 0],
[100, 110, 0],
[300, 70, 0],
[160, -90, 0],
[190, -300, 0],
[0, -210, 0],
[-190, -300, 0],
[-160, -90, 0],
[-300, 70, 0],
[-100, 110, 0],
]
)
if __name__ == "__main__":
print("Generating polygon object...")
polygon = BoundaryPolygon(star)
print("Plotting object...")
polygon.plot2D()
def square():
square = np.array([[0, 0, 0], [0.0, 1.0, 0.0], [1.0, 1.0, 0.0], [1.0, 0.0, 0.0]])
polygon = BoundaryPolygon(square * 20)
return polygon
def __init__(self, polygon_array, lattice, gridsize=0.1):
self.polygon = np.concatenate(
[polygon_array, np.array([polygon_array[0, :]])], axis=0)
self.lattice = lattice
self.obj = BoundaryPolygon(polygon_array)
_ = self.inside