alhambra.flatish

Tiles, seeds, glues, and lattices for the ‘flatish’ tile motif.

Module Contents

Classes

FlatishSingleTile9	Flatish single tile, with domains (5'→3') of 12, 9, 11, and 10 nt. North edge is 9nt.
FlatishSingleTile10	Flatish single tile, with domains (5'→3') of 11, 10, 12, and 9 nt. North edge is 10nt.
FlatishVDupleTile10_E2	Base class for a tile.
FlatishVDupleTile9_E2	Base class for a tile.
FlatishHDupleTile9_E	Base class for a tile.
FlatishHDupleTile10_E	Base class for a tile.
FlatishHSeed9	Flatish origami seed.
FlatishVSeed9	Flatish origami seed (vertical).

class alhambra.flatish.FlatishSingleTile9(edges: Iterable[alhambra.glues.Glue | str] | None = None, name: str | None = None, color: Color | None = None, stoic: float | None = None, note: str | dict[str, Any] | None = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None)

Bases: alhambra.tiles.BaseSSTSingle

Flatish single tile, with domains (5’→3’) of 12, 9, 11, and 10 nt. North edge is 9nt.

_base_domains: ClassVar[list[alhambra.tiles.SSGlue]]

_scadnano_offsets = ((), (), (1, 11), (1,))

_scadnano_5p_offset = (0, 21)

class alhambra.flatish.FlatishSingleTile10(edges: Iterable[alhambra.glues.Glue | str] | None = None, name: str | None = None, color: Color | None = None, stoic: float | None = None, note: str | dict[str, Any] | None = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None)

Bases: alhambra.tiles.BaseSSTSingle

Flatish single tile, with domains (5’→3’) of 11, 10, 12, and 9 nt. North edge is 10nt.

_base_domains: ClassVar[list[alhambra.tiles.SSGlue]]

_scadnano_offsets = ((), (), (1, 12), (1,))

_scadnano_5p_offset = (0, 21)

class alhambra.flatish.FlatishVDupleTile10_E2(edges: Iterable[alhambra.glues.Glue | str] | None = None, name: str | None = None, color: Color | None = None, stoic: float | None = None, note: str | dict[str, Any] | None = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None)

Bases: alhambra.tiles.VDupleTile, alhambra.tiles.BaseSSTile

Base class for a tile.

property domains: list[alhambra.tiles.SSGlue]

_base_domains: ClassVar[list[alhambra.tiles.SSGlue]]

_base_edges

_scadnano_offsets = ((), (), (0, 21), (2, 23), (2, 1), (1,))

_scadnano_5p_offset = (1, 33)

to_scadnano(design: scadnano.Design, helix: int, offset: int) → scadnano.Strand

_input_neighborhood_domains() → Sequence[tuple[Sequence[str], Sequence[str]]]

class alhambra.flatish.FlatishVDupleTile9_E2(edges: Iterable[alhambra.glues.Glue | str] | None = None, name: str | None = None, color: Color | None = None, stoic: float | None = None, note: str | dict[str, Any] | None = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None)

Bases: alhambra.tiles.VDupleTile, alhambra.tiles.BaseSSTile

Base class for a tile.

property domains

_base_domains: ClassVar[list[alhambra.tiles.SSGlue]]

_base_edges

_scadnano_offsets = ((), (), (0, 21), (2, 23), (2, 2), (1,))

_scadnano_5p_offset = (1, 32)

to_scadnano(design: scadnano.Design, helix: int, offset: int) → scadnano.Strand

_input_neighborhood_domains() → Sequence[tuple[Sequence[str], Sequence[str]]]

class alhambra.flatish.FlatishHDupleTile9_E(edges: Iterable[alhambra.glues.Glue | str] | None = None, name: str | None = None, color: Color | None = None, stoic: float | None = None, note: str | dict[str, Any] | None = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None)

Bases: alhambra.tiles.HDupleTile, alhambra.tiles.BaseSSTile

Base class for a tile.

property domains

_base_domains: list[alhambra.tiles.SSGlue]

_base_edges

_scadnano_5p_offset = ()

to_scadnano(design: scadnano.Design, helix: int, offset: int) → scadnano.Strand

_input_neighborhood_domains() → Sequence[tuple[Sequence[str], Sequence[str]]]

class alhambra.flatish.FlatishHDupleTile10_E(edges: Iterable[alhambra.glues.Glue | str] | None = None, name: str | None = None, color: Color | None = None, stoic: float | None = None, note: str | dict[str, Any] | None = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None)

Bases: alhambra.tiles.HDupleTile, alhambra.tiles.BaseSSTile

Base class for a tile.

property domains

_base_domains: ClassVar[list[alhambra.tiles.SSGlue]]

_base_edges

_scadnano_5p_offset = ()

to_scadnano(design: scadnano.Design, helix: int, offset: int) → scadnano.Strand

_input_neighborhood_domains() → Sequence[tuple[Sequence[str], Sequence[str]]]

class alhambra.flatish.FlatishHSeed9(adapter_tiles: Sequence[tuple[alhambra.glues.Glue | str, FlatishSingleTile9]] = tuple())

Bases: alhambra.seeds.Seed

Flatish origami seed.

adapter_tiles: list[tuple[alhambra.glues.Glue | str, FlatishSingleTile9]]

to_dict(glues_as_refs: bool = False) → dict

classmethod from_dict(d: dict) → T_FHS9

to_xgrow(gluenamemap: Callable[[str], str] = lambda x: ..., offset: tuple[int, int] | None = None, xgtiles: Sequence[xgrow.tileset.Tile] | None = None) → tuple[list[xgrow.tileset.Tile], list[xgrow.tileset.Bond], xgrow.tileset.InitState]

Create xgrow implementation of the seed.

Converts the Seed to a list of xgrow tiles to add to a system, a list of bonds to add, and an initial state.

class alhambra.flatish.FlatishVSeed9(adapter_tiles: Sequence[tuple[alhambra.glues.Glue | str, FlatishSingleTile9]] = tuple())

Bases: alhambra.seeds.Seed

Flatish origami seed (vertical).

adapter_tiles: list[tuple[alhambra.glues.Glue | str, FlatishSingleTile9]]

to_dict(glues_as_refs: bool = False) → dict

classmethod from_dict(d: dict) → FlatishVSeed9

to_xgrow(gluenamemap: Callable[[str], str] = lambda x: ..., offset: tuple[int, int] | None = None, xgtiles: Sequence[xgrow.tileset.Tile] | None = None) → tuple[list[xgrow.tileset.Tile], list[xgrow.tileset.Bond], xgrow.tileset.InitState]

Create xgrow implementation of the seed.

Converts the Seed to a list of xgrow tiles to add to a system, a list of bonds to add, and an initial state.