alhambra.grid

Module Contents

Classes

Lattice	Helper class that provides a standard way to create an ABC using
AbstractLattice	Helper class that provides a standard way to create an ABC using
LatticeSupportingScadnano	Helper class that provides a standard way to create an ABC using
AbstractLatticeSupportingScadnano	Helper class that provides a standard way to create an ABC using
ScadnanoLattice	Helper class that provides a standard way to create an ABC using
SSTLattice	A lattice of flatish tiles. Position 0,0 is a 10nt-north tile.
LatticeFactory

Functions

_skip_polyT_and_inertname(→ bool)
sst_10_11_hofromxy(→ tuple[int, int])

Attributes

AL
lattice_factory

class alhambra.grid.Lattice

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

abstract property seed: alhambra.seeds.Seed | None

abstract __getitem__(index) → str | Any

abstract __setitem__(index, v)

abstract asdict() → dict[str, Any]

classmethod fromdict(d: dict[str, Any]) → Lattice

class alhambra.grid.AbstractLattice(v: AbstractLattice | numpy.ndarray, seed: alhambra.seeds.Seed | None = None, seed_offset: tuple[int, int] | None = None)

Bases: Lattice

Helper class that provides a standard way to create an ABC using inheritance.

property tilenames: list[str]

grid: numpy.ndarray

seed: alhambra.seeds.Seed | None

seed_offset: tuple[int, int] = (0, 0)

__getitem__(index) → str | Any

__setitem__(index, v)

asdict() → dict[str, Any]

classmethod fromdict(d: dict[str, Any]) → AL

classmethod empty(shape)

class alhambra.grid.LatticeSupportingScadnano

Bases: Lattice

Helper class that provides a standard way to create an ABC using inheritance.

seed: alhambra.seeds.SeedSupportingScadnano | None

abstract to_scadnano_lattice() → ScadnanoLattice

to_scadnano(tileset: alhambra.tilesets.TileSet) → scadnano.Design

class alhambra.grid.AbstractLatticeSupportingScadnano(v: AbstractLattice | numpy.ndarray, seed: alhambra.seeds.Seed | None = None, seed_offset: tuple[int, int] | None = None)

Bases: AbstractLattice

Helper class that provides a standard way to create an ABC using inheritance.

seed: alhambra.seeds.SeedSupportingScadnano | None

abstract to_scadnano_lattice() → ScadnanoLattice

to_scadnano(tileset: alhambra.tilesets.TileSet) → scadnano.Design

class alhambra.grid.ScadnanoLattice

Bases: LatticeSupportingScadnano

Helper class that provides a standard way to create an ABC using inheritance.

positions: dict[tuple[int, int], str]

seed: alhambra.seeds.SeedSupportingScadnano | None

seed_position: tuple[int, int] = (0, 0)

__getitem__(index: tuple[int, int]) → str | None

__setitem__(index: tuple[int, int], v: str)

findtile(tile: str | alhambra.tiles.Tile) → list[tuple[int, int]]

to_scadnano_lattice() → ScadnanoLattice

abstract asdict() → dict[str, Any]

classmethod fromdict(d: dict[str, Any])

alhambra.grid.AL

alhambra.grid._skip_polyT_and_inertname(glue: alhambra.glues.Glue) → bool

alhambra.grid.sst_10_11_hofromxy(x: int, y: int, start_helix: int, start_o: int, p: Literal[10, 11] = 10) → tuple[int, int]

class alhambra.grid.SSTLattice(v: AbstractLattice | numpy.ndarray, seed: alhambra.seeds.Seed | None = None, seed_offset: tuple[int, int] | None = None)

Bases: AbstractLatticeSupportingScadnano

A lattice of flatish tiles. Position 0,0 is a 10nt-north tile.

to_scadnano_lattice() → ScadnanoLattice

class alhambra.grid.LatticeFactory

types: dict[str, Type[Lattice]]

register(c: Type[Lattice], n: str | None = None)

from_dict(d: dict[str, Any]) → Lattice

alhambra.grid.lattice_factory