:py:mod:`alhambra.tiles` ======================== .. py:module:: alhambra.tiles Module Contents --------------- Classes ~~~~~~~ .. autoapisummary:: alhambra.tiles.D alhambra.tiles.EdgeLoc alhambra.tiles.EdgeView alhambra.tiles.UseView alhambra.tiles.Tile alhambra.tiles.TileSupportingScadnano alhambra.tiles.SingleTile alhambra.tiles.VDupleTile alhambra.tiles.HDupleTile alhambra.tiles.SupportsGuards alhambra.tiles.BaseSSTile alhambra.tiles.BaseSSTSingle alhambra.tiles.BaseSSTSingleWithExtensions alhambra.tiles.SST10_5S alhambra.tiles.SST11_5S alhambra.tiles.SST10 alhambra.tiles.SST11 alhambra.tiles.TileFactory alhambra.tiles.TileList alhambra.tiles.DAOETile alhambra.tiles.DAOESingle alhambra.tiles.DAOESingle5p alhambra.tiles.DAOESingle3p alhambra.tiles.DAOEHDouble3p alhambra.tiles.DAOEHDouble5p alhambra.tiles.DAOEVDouble3p alhambra.tiles.DAOEVDouble5p Functions ~~~~~~~~~ .. autoapisummary:: alhambra.tiles._scadnano_color Attributes ~~~~~~~~~~ .. autoapisummary:: alhambra.tiles.Color alhambra.tiles.T alhambra.tiles.log alhambra.tiles.Offset alhambra.tiles.EL alhambra.tiles.Domain alhambra.tiles.tile_factory alhambra.tiles.SomeTile .. py:data:: Color .. py:data:: T .. py:data:: log .. py:class:: D Bases: :py:obj:`enum.Enum` Cardinal directions; also edge directions for single tiles. .. py:property:: complement :type: D .. py:attribute:: N :value: 0 .. py:attribute:: E :value: 1 .. py:attribute:: S :value: 2 .. py:attribute:: W :value: 3 .. py:data:: Offset .. py:class:: EdgeLoc .. py:attribute:: direction :type: D .. py:attribute:: position :type: Offset :value: (0, 0) .. py:data:: EL .. py:class:: EdgeView(_edges: List[alhambra.glues.Glue], _tile: Tile) A class to ensure that tile edge glue manipulations are handled through the tile. .. py:attribute:: _edges :type: List[alhambra.glues.Glue] .. py:attribute:: _tile :type: Tile .. py:attribute:: __slots__ :value: ('_edges', '_tile') .. py:method:: __getitem__(k: int | str) -> alhambra.glues.Glue __getitem__(k: slice) -> list[alhambra.glues.Glue] .. py:method:: __setitem__(k: int | str, v: alhambra.glues.Glue) -> None .. py:method:: insert(index: int, value: alhambra.glues.Glue) -> None .. py:method:: __delitem__(k: int | str) -> None :abstractmethod: .. py:method:: __iter__() -> Iterator[alhambra.glues.Glue] .. py:method:: __next__() -> Generator[alhambra.glues.Glue, None, None] .. py:method:: __len__() -> int .. py:method:: __repr__() -> str Return repr(self). .. py:method:: __str__() -> str Return str(self). .. py:class:: UseView(_tile: Tile) Bases: :py:obj:`MutableMapping`\ [\ :py:obj:`int`\ , :py:obj:`alhambra.glues.Use`\ ] A class to ensure that tile edge use manipulations are handled through the tile. .. py:attribute:: _tile :type: Tile .. py:attribute:: __slots__ :value: '_tile' .. py:method:: __getitem__(k: int) -> alhambra.glues.Use __getitem__(k: slice) -> list[alhambra.glues.Use] .. py:method:: __setitem__(k: int, v: alhambra.glues.Use) -> None .. py:method:: insert(index: int, value: alhambra.glues.Use) -> None :abstractmethod: .. py:method:: __len__() -> int .. py:method:: __repr__() -> str Return repr(self). .. py:method:: __str__() -> str Return str(self). .. py:class:: Tile(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Base class for a tile. .. py:property:: structure .. py:property:: use :type: Sequence[alhambra.glues.Use] .. py:property:: edges :type: EdgeView .. py:property:: edge_directions :type: List[D] :abstractmethod: .. py:property:: edge_locations :type: List[EdgeLoc] :abstractmethod: .. py:property:: rotations :type: List[Tile] :abstractmethod: .. py:property:: is_fake :type: bool .. py:property:: xgname :type: str .. py:attribute:: name :type: Optional[str] .. py:attribute:: _edges :type: List[alhambra.glues.Glue] .. py:attribute:: color :type: Optional[Color] .. py:attribute:: stoic :type: Optional[float] .. py:attribute:: note :type: Optional[str | dict[str, Any]] .. py:attribute:: fake :type: bool .. py:attribute:: uses :type: List[List[alhambra.glues.Use]] .. py:attribute:: __slots__ :value: ('name', '_edges', 'color', 'stoic', 'note', 'fake', 'uses') .. py:method:: get_concentration(base_concentration: float) -> float .. py:method:: get_stoic(base_concentration: float) -> float Returns the stoichiometric ratio of this tile to the base concentration. .. py:method:: set_edge(i: int, glue: alhambra.glues.Glue) -> None .. py:method:: copy() -> T .. py:method:: _get_edge_index(v: str) -> int :classmethod: :abstractmethod: .. py:method:: ident() -> str .. py:method:: merge(other) -> Tile .. py:method:: to_dict(refglues: set[str] = set()) -> dict[str, Any] .. py:method:: update_glues(gluedict: alhambra.glues.GlueList[alhambra.glues.Glue]) -> None .. py:method:: update_glues_and_list(gluedict: alhambra.glues.GlueList[alhambra.glues.Glue]) -> None .. py:method:: from_dict(d: dict[str, Any]) -> Tile :staticmethod: .. py:method:: to_xgrow(gluenamemap: Callable[[str], str] = lambda x: x) -> xgrow.tileset.Tile .. py:method:: abstract_diagram(tileset: alhambra.tilesets.TileSet | None = None, draw_names: bool = True, draw_glues: bool = True) -> alhambra.drawing.Group :abstractmethod: .. py:class:: TileSupportingScadnano(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str] = None, domains: Optional[Iterable[alhambra.glues.SSGlue]] = None) Bases: :py:obj:`abc.ABC`, :py:obj:`Tile` Abstract base class for a tile that allows export to scadnano. .. py:property:: _scadnano_5p_offset :type: tuple[int, int] :abstractmethod: .. py:method:: to_scadnano(design: scadnano.Design, helix: int, offset: int) -> scadnano.Strand :abstractmethod: .. py:class:: SingleTile(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`Tile` A tile with N, E, S and W edges. .. py:property:: edge_directions :type: List[D] .. py:property:: edge_locations :type: List[EdgeLoc] .. py:method:: _get_edge_index(v: str) -> int :classmethod: .. py:method:: abstract_diagram(tileset: alhambra.tilesets.TileSet | None = None, draw_names: bool = True, draw_glues: bool = True) -> alhambra.drawing.Group .. py:class:: VDupleTile(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`Tile` Base class for a tile. .. py:property:: edge_directions :type: List[D] .. py:property:: edge_locations :type: List[EdgeLoc] .. py:method:: to_xgrow(gluenamemap: Callable[[str], str] = lambda x: x) -> xgrow.tileset.Tile .. py:method:: _get_edge_index(v: str) -> int :classmethod: .. py:method:: abstract_diagram(tileset: alhambra.tilesets.TileSet | None = None, draw_names: bool = True, draw_glues: bool = True) -> alhambra.drawing.Group .. py:class:: HDupleTile(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`Tile` Base class for a tile. .. py:property:: edge_directions :type: List[D] .. py:property:: edge_locations :type: List[EdgeLoc] .. py:method:: to_xgrow(gluenamemap: Callable[[str], str] = lambda x: x) -> xgrow.tileset.Tile .. py:method:: _get_edge_index(v: str) -> int :classmethod: .. py:method:: abstract_diagram(tileset: alhambra.tilesets.TileSet | None = None, draw_names: bool = True, draw_glues: bool = True) -> alhambra.drawing.Group .. py:class:: SupportsGuards .. py:method:: create_guards(directions: Collection[str | D] = (D.E, D.S)) -> list[alhambra.glues.Glue] :abstractmethod: .. py:class:: BaseSSTile(edges: Optional[List[Union[str, alhambra.glues.Glue]]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, sequence: Optional[alhambra.seq.Seq] = None, domains: Optional[Sequence[alhambra.glues.SSGlue]] = None, note: Optional[str] = None, use: Optional[Sequence[alhambra.glues.Use]] = None, uses: Optional[Sequence[Sequence[alhambra.glues.Use]]] = None) Bases: :py:obj:`SupportsGuards`, :py:obj:`TileSupportingScadnano` Base class for single-stranded tiles. .. py:property:: _base_domains :type: List[alhambra.glues.SSGlue] :abstractmethod: .. py:property:: _base_edges :type: List[alhambra.glues.SSGlue] :abstractmethod: .. py:property:: domains :type: List[alhambra.glues.SSGlue] :abstractmethod: .. py:property:: edge_directions :type: list[D] :abstractmethod: .. py:property:: _sequence_length :type: int .. py:property:: sequence :type: alhambra.seq.Seq .. py:property:: edges .. py:attribute:: _edges :type: List[alhambra.glues.Glue] .. py:method:: to_dict(refglues: set[str] = set()) -> dict[str, Any] .. py:method:: _input_neighborhood_domains() -> Sequence[Tuple[Sequence[str], Sequence[str]]] :abstractmethod: .. py:method:: set_edge(i: int, glue: alhambra.glues.Glue) -> None .. py:method:: __repr__() -> str Return repr(self). .. py:method:: __str__() -> str Return str(self). .. py:method:: create_guards(directions: Collection[str | D] = (D.E, D.S)) -> list[alhambra.glues.Glue] .. py:function:: _scadnano_color(color: Optional[str]) -> Optional[scadnano.Color] .. py:class:: BaseSSTSingle(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`SingleTile`, :py:obj:`BaseSSTile` Base class for a standard-orientation SST single tile. .. py:property:: domains :type: List[alhambra.glues.SSGlue] .. py:property:: _base_edges :type: List[alhambra.glues.SSGlue] .. py:attribute:: _edges :type: List[alhambra.glues.Glue] .. py:method:: _input_neighborhood_domains() -> Sequence[Tuple[Sequence[str], Sequence[str]]] .. py:method:: to_scadnano(design: scadnano.Design, helix: int, offset: int) -> scadnano.Strand .. py:data:: Domain .. py:class:: BaseSSTSingleWithExtensions(edges: Optional[list[Union[str, alhambra.glues.Glue]]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, sequence: Optional[alhambra.seq.Seq] = None, domains: Optional[list[Domain]] = None, note: Optional[str] = None, use: Optional[Sequence[alhambra.glues.Use]] = None, uses: Optional[Sequence[Sequence[alhambra.glues.Use]]] = None, mod5: alhambra.seq.Seq | str | int | dict | None = None, mod3: alhambra.seq.Seq | str | int | dict | None = None) Bases: :py:obj:`BaseSSTSingle` Base class for a standard-orientation SST single tile. .. py:property:: domains :type: List[alhambra.glues.SSGlue] .. py:property:: _sequence_length :type: int .. py:property:: sequence :type: alhambra.seq.Seq .. py:attribute:: mod5 :type: Domain | None .. py:attribute:: mod3 :type: Domain | None .. py:method:: to_dict(refglues: set[str] = set()) -> dict[str, Any] .. py:class:: SST10_5S(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`BaseSSTSingle` Single SST, with domains (5'→3') of 11, 10, 10, and 11 nt. North edge is 10nt. 5' is S, 3' is E. .. py:property:: domains :type: List[alhambra.glues.SSGlue] .. py:property:: _base_edges :type: List[alhambra.glues.SSGlue] .. py:attribute:: _base_domains :type: ClassVar[list[alhambra.glues.SSGlue]] .. py:attribute:: _scadnano_offsets :value: ((), (), (1, 10), (1,)) .. py:attribute:: _scadnano_5p_offset :value: (1, 21) .. py:class:: SST11_5S(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`BaseSSTSingle` Single SST, with domains (5'→3') of 10, 11, 11, and 10 nt. North edge is 11nt. 5' is S, 3' is E. .. py:property:: domains :type: List[alhambra.glues.SSGlue] .. py:property:: _base_edges :type: List[alhambra.glues.SSGlue] .. py:attribute:: _base_domains :type: ClassVar[list[alhambra.glues.SSGlue]] .. py:attribute:: _scadnano_offsets :value: ((), (), (1, 11), (1,)) .. py:attribute:: _scadnano_5p_offset :value: (1, 21) .. py:class:: SST10(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`BaseSSTSingle` Single SST, with domains (5'→3') of 11, 10, 10, and 11 nt. North edge is 10nt. 5' is E, 3' is S. .. py:attribute:: _base_domains :type: ClassVar[list[alhambra.glues.SSGlue]] .. py:attribute:: _scadnano_offsets :value: ((), (), (1, 10), (1,)) .. py:attribute:: _scadnano_5p_offset :value: (1, 21) .. py:class:: SST11(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`BaseSSTSingle` Single SST, with domains (5'→3') of 10, 11, 11, and 10 nt. North edge is 11nt. 5' is E, 3' is S. .. py:attribute:: _base_domains :type: ClassVar[list[alhambra.glues.SSGlue]] .. py:attribute:: _scadnano_offsets :value: ((), (), (1, 11), (1,)) .. py:attribute:: _scadnano_5p_offset :value: (1, 21) .. py:class:: TileFactory .. py:attribute:: types :type: dict[str, Type[Tile]] .. py:method:: register(c: Type[Tile], n: Optional[str] = None) -> None .. py:method:: from_dict(d: dict[str, Any]) -> Tile .. py:method:: from_scadnano(d: scadnano.Strand | Iterable[scadnano.Strand], return_position: Literal[True]) -> tuple[TileSupportingScadnano, tuple[int, int]] from_scadnano(d: scadnano.Strand | Iterable[scadnano.Strand], return_position: Literal[False]) -> TileSupportingScadnano .. py:data:: tile_factory .. py:data:: SomeTile .. py:class:: TileList(initial: Iterable[T_NMI] = tuple()) Bases: :py:obj:`Generic`\ [\ :py:obj:`SomeTile`\ ], :py:obj:`alhambra.classes.UpdateListD`\ [\ :py:obj:`SomeTile`\ ] Abstract base class for generic types. A generic type is typically declared by inheriting from this class parameterized with one or more type variables. For example, a generic mapping type might be defined as:: class Mapping(Generic[KT, VT]): def __getitem__(self, key: KT) -> VT: ... # Etc. This class can then be used as follows:: def lookup_name(mapping: Mapping[KT, VT], key: KT, default: VT) -> VT: try: return mapping[key] except KeyError: return default .. py:method:: glues_from_tiles() -> alhambra.glues.GlueList .. py:method:: domains_from_tiles() -> alhambra.glues.GlueList .. py:class:: DAOETile(name: str, sequence: str | None = None, sequences: list[str] | None = None, edges: List[alhambra.glues.Glue | str] | None = None, label: str | None = None, color: str | None = None, **kwargs) Bases: :py:obj:`Tile` Base class for a tile. .. py:attribute:: _edges :type: List[alhambra.glues.Glue] .. py:attribute:: _strand_sequences :type: List[str] | None .. py:method:: to_dict(refglues: set[str] = set()) -> dict[str, Any] .. py:class:: DAOESingle(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`SingleTile`, :py:obj:`DAOETile` A tile with N, E, S and W edges. .. py:class:: DAOESingle5p(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`DAOESingle` A tile with N, E, S and W edges. .. py:attribute:: _baseglues :type: ClassVar[List[alhambra.glues.DXGlue]] .. py:attribute:: _gluelocs :value: [(0,), (3,), (3,), (0,)] .. py:class:: DAOESingle3p(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`DAOESingle` A tile with N, E, S and W edges. .. py:attribute:: _baseglues :type: ClassVar[List[alhambra.glues.DXGlue]] .. py:attribute:: _gluelocs :value: [(0,), (3,), (3,), (0,)] .. py:class:: DAOEHDouble3p(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`HDupleTile`, :py:obj:`DAOETile` Base class for a tile. .. py:class:: DAOEHDouble5p(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`HDupleTile`, :py:obj:`DAOETile` Base class for a tile. .. py:class:: DAOEVDouble3p(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`VDupleTile`, :py:obj:`DAOETile` Base class for a tile. .. py:class:: DAOEVDouble5p(edges: Optional[Iterable[alhambra.glues.Glue | str]] = None, name: Optional[str] = None, color: Optional[Color] = None, stoic: Optional[float] = None, note: Optional[str | dict[str, Any]] = None, use: Sequence[alhambra.glues.Use | int | str] | None = None, fake: bool = False, uses: Sequence[Sequence[alhambra.glues.Use | int | str]] | None = None) Bases: :py:obj:`VDupleTile`, :py:obj:`DAOETile` Base class for a tile.