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()