alhambra.tiles

Module Contents

Classes

D	Cardinal directions; also edge directions for single tiles.
EdgeLoc
EdgeView	A class to ensure that tile edge glue manipulations are handled through the tile.
UseView	A class to ensure that tile edge use manipulations are handled through the tile.
Tile	Base class for a tile.
TileSupportingScadnano	Abstract base class for a tile that allows export to scadnano.
SingleTile	A tile with N, E, S and W edges.
VDupleTile	Base class for a tile.
HDupleTile	Base class for a tile.
SupportsGuards
BaseSSTile	Base class for single-stranded tiles.
BaseSSTSingle	Base class for a standard-orientation SST single tile.
BaseSSTSingleWithExtensions	Base class for a standard-orientation SST single tile.
SST10_5S	Single SST, with domains (5'→3') of 11, 10, 10, and 11 nt. North edge is 10nt. 5' is S, 3' is E.
SST11_5S	Single SST, with domains (5'→3') of 10, 11, 11, and 10 nt. North edge is 11nt. 5' is S, 3' is E.
SST10	Single SST, with domains (5'→3') of 11, 10, 10, and 11 nt. North edge is 10nt. 5' is E, 3' is S.
SST11	Single SST, with domains (5'→3') of 10, 11, 11, and 10 nt. North edge is 11nt. 5' is E, 3' is S.
TileFactory
TileList	Abstract base class for generic types.
DAOETile	Base class for a tile.
DAOESingle	A tile with N, E, S and W edges.
DAOESingle5p	A tile with N, E, S and W edges.
DAOESingle3p	A tile with N, E, S and W edges.
DAOEHDouble3p	Base class for a tile.
DAOEHDouble5p	Base class for a tile.
DAOEVDouble3p	Base class for a tile.
DAOEVDouble5p	Base class for a tile.

Functions

_scadnano_color(→ Optional[scadnano.Color])

Attributes

Color
T
log
Offset
EL
Domain
tile_factory
SomeTile

alhambra.tiles.Color

alhambra.tiles.T

alhambra.tiles.log

class alhambra.tiles.D

Bases: enum.Enum

Cardinal directions; also edge directions for single tiles.

property complement: D

N = 0

E = 1

S = 2

W = 3

alhambra.tiles.Offset

class alhambra.tiles.EdgeLoc

direction: D

position: Offset = (0, 0)

alhambra.tiles.EL

class alhambra.tiles.EdgeView(_edges: List[alhambra.glues.Glue], _tile: Tile)

A class to ensure that tile edge glue manipulations are handled through the tile.

_edges: List[alhambra.glues.Glue]

_tile: Tile

__slots__ = ('_edges', '_tile')

__getitem__(k: int | str) → alhambra.glues.Glue

__getitem__(k: slice) → list[alhambra.glues.Glue]

__setitem__(k: int | str, v: alhambra.glues.Glue) → None

insert(index: int, value: alhambra.glues.Glue) → None

abstract __delitem__(k: int | str) → None

__iter__() → Iterator[alhambra.glues.Glue]

__next__() → Generator[alhambra.glues.Glue, None, None]

__len__() → int

__repr__() → str

Return repr(self).

__str__() → str

Return str(self).

class alhambra.tiles.UseView(_tile: Tile)

Bases: MutableMapping[int, alhambra.glues.Use]

A class to ensure that tile edge use manipulations are handled through the tile.

_tile: Tile

__slots__ = '_tile'

__getitem__(k: int) → alhambra.glues.Use

__getitem__(k: slice) → list[alhambra.glues.Use]

__setitem__(k: int, v: alhambra.glues.Use) → None

abstract insert(index: int, value: alhambra.glues.Use) → None

__len__() → int

__repr__() → str

Return repr(self).

__str__() → str

Return str(self).

class alhambra.tiles.Tile(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)

Base class for a tile.

property structure

property use: Sequence[alhambra.glues.Use]

property edges: EdgeView

abstract property edge_directions: List[D]

abstract property edge_locations: List[EdgeLoc]

abstract property rotations: List[Tile]

property is_fake: bool

property xgname: str

name: str | None

_edges: List[alhambra.glues.Glue]

color: Color | None

stoic: float | None

note: str | dict[str, Any] | None

fake: bool

uses: List[List[alhambra.glues.Use]]

__slots__ = ('name', '_edges', 'color', 'stoic', 'note', 'fake', 'uses')

get_concentration(base_concentration: float) → float

get_stoic(base_concentration: float) → float

Returns the stoichiometric ratio of this tile to the base concentration.

set_edge(i: int, glue: alhambra.glues.Glue) → None

copy() → T

abstract classmethod _get_edge_index(v: str) → int

ident() → str

merge(other) → Tile

to_dict(refglues: set[str] = set()) → dict[str, Any]

update_glues(gluedict: alhambra.glues.GlueList[alhambra.glues.Glue]) → None

update_glues_and_list(gluedict: alhambra.glues.GlueList[alhambra.glues.Glue]) → None

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

to_xgrow(gluenamemap: Callable[[str], str] = lambda x: ...) → xgrow.tileset.Tile

abstract abstract_diagram(tileset: alhambra.tilesets.TileSet | None = None, draw_names: bool = True, draw_glues: bool = True) → alhambra.drawing.Group

class alhambra.tiles.TileSupportingScadnano(edges: Iterable[alhambra.glues.Glue | str] | None = None, name: str | None = None, color: Color | None = None, stoic: float | None = None, note: str | None = None, domains: Iterable[alhambra.glues.SSGlue] | None = None)

Bases: abc.ABC, Tile

Abstract base class for a tile that allows export to scadnano.

abstract property _scadnano_5p_offset: tuple[int, int]

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

class alhambra.tiles.SingleTile(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: Tile

A tile with N, E, S and W edges.

property edge_directions: List[D]

property edge_locations: List[EdgeLoc]

classmethod _get_edge_index(v: str) → int

abstract_diagram(tileset: alhambra.tilesets.TileSet | None = None, draw_names: bool = True, draw_glues: bool = True) → alhambra.drawing.Group

class alhambra.tiles.VDupleTile(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: Tile

Base class for a tile.

property edge_directions: List[D]

property edge_locations: List[EdgeLoc]

to_xgrow(gluenamemap: Callable[[str], str] = lambda x: ...) → xgrow.tileset.Tile

classmethod _get_edge_index(v: str) → int

abstract_diagram(tileset: alhambra.tilesets.TileSet | None = None, draw_names: bool = True, draw_glues: bool = True) → alhambra.drawing.Group

class alhambra.tiles.HDupleTile(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: Tile

Base class for a tile.

property edge_directions: List[D]

property edge_locations: List[EdgeLoc]

to_xgrow(gluenamemap: Callable[[str], str] = lambda x: ...) → xgrow.tileset.Tile

classmethod _get_edge_index(v: str) → int

abstract_diagram(tileset: alhambra.tilesets.TileSet | None = None, draw_names: bool = True, draw_glues: bool = True) → alhambra.drawing.Group

class alhambra.tiles.SupportsGuards

abstract create_guards(directions: Collection[str | D] = (D.E, D.S)) → list[alhambra.glues.Glue]

class alhambra.tiles.BaseSSTile(edges: List[str | alhambra.glues.Glue] | None = None, name: str | None = None, color: Color | None = None, stoic: float | None = None, sequence: alhambra.seq.Seq | None = None, domains: Sequence[alhambra.glues.SSGlue] | None = None, note: str | None = None, use: Sequence[alhambra.glues.Use] | None = None, uses: Sequence[Sequence[alhambra.glues.Use]] | None = None)

Bases: SupportsGuards, TileSupportingScadnano

Base class for single-stranded tiles.

abstract property _base_domains: List[alhambra.glues.SSGlue]

abstract property _base_edges: List[alhambra.glues.SSGlue]

abstract property domains: List[alhambra.glues.SSGlue]

abstract property edge_directions: list[D]

property _sequence_length: int

property sequence: alhambra.seq.Seq

property edges

_edges: List[alhambra.glues.Glue]

to_dict(refglues: set[str] = set()) → dict[str, Any]

abstract _input_neighborhood_domains() → Sequence[Tuple[Sequence[str], Sequence[str]]]

set_edge(i: int, glue: alhambra.glues.Glue) → None

__repr__() → str

Return repr(self).

__str__() → str

Return str(self).

create_guards(directions: Collection[str | D] = (D.E, D.S)) → list[alhambra.glues.Glue]

alhambra.tiles._scadnano_color(color: str | None) → scadnano.Color | None

class alhambra.tiles.BaseSSTSingle(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: SingleTile, BaseSSTile

Base class for a standard-orientation SST single tile.

property domains: List[alhambra.glues.SSGlue]

property _base_edges: List[alhambra.glues.SSGlue]

_edges: List[alhambra.glues.Glue]

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

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

alhambra.tiles.Domain

class alhambra.tiles.BaseSSTSingleWithExtensions(edges: list[str | alhambra.glues.Glue] | None = None, name: str | None = None, color: Color | None = None, stoic: float | None = None, sequence: alhambra.seq.Seq | None = None, domains: list[Domain] | None = None, note: str | None = None, use: Sequence[alhambra.glues.Use] | None = None, uses: Sequence[Sequence[alhambra.glues.Use]] | None = None, mod5: alhambra.seq.Seq | str | int | dict | None = None, mod3: alhambra.seq.Seq | str | int | dict | None = None)

Bases: BaseSSTSingle

Base class for a standard-orientation SST single tile.

property domains: List[alhambra.glues.SSGlue]

property _sequence_length: int

property sequence: alhambra.seq.Seq

mod5: Domain | None

mod3: Domain | None

to_dict(refglues: set[str] = set()) → dict[str, Any]

class alhambra.tiles.SST10_5S(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: BaseSSTSingle

Single SST, with domains (5’→3’) of 11, 10, 10, and 11 nt. North edge is 10nt. 5’ is S, 3’ is E.

property domains: List[alhambra.glues.SSGlue]

property _base_edges: List[alhambra.glues.SSGlue]

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

_scadnano_offsets = ((), (), (1, 10), (1,))

_scadnano_5p_offset = (1, 21)

class alhambra.tiles.SST11_5S(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: BaseSSTSingle

Single SST, with domains (5’→3’) of 10, 11, 11, and 10 nt. North edge is 11nt. 5’ is S, 3’ is E.

property domains: List[alhambra.glues.SSGlue]

property _base_edges: List[alhambra.glues.SSGlue]

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

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

_scadnano_5p_offset = (1, 21)

class alhambra.tiles.SST10(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: BaseSSTSingle

Single SST, with domains (5’→3’) of 11, 10, 10, and 11 nt. North edge is 10nt. 5’ is E, 3’ is S.

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

_scadnano_offsets = ((), (), (1, 10), (1,))

_scadnano_5p_offset = (1, 21)

class alhambra.tiles.SST11(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: BaseSSTSingle

Single SST, with domains (5’→3’) of 10, 11, 11, and 10 nt. North edge is 11nt. 5’ is E, 3’ is S.

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

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

_scadnano_5p_offset = (1, 21)

class alhambra.tiles.TileFactory

types: dict[str, Type[Tile]]

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

from_dict(d: dict[str, Any]) → Tile

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

alhambra.tiles.tile_factory

alhambra.tiles.SomeTile

class alhambra.tiles.TileList(initial: Iterable[T_NMI] = tuple())

Bases: Generic[SomeTile], alhambra.classes.UpdateListD[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

glues_from_tiles() → alhambra.glues.GlueList

domains_from_tiles() → alhambra.glues.GlueList

class alhambra.tiles.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: Tile

Base class for a tile.

_edges: List[alhambra.glues.Glue]

_strand_sequences: List[str] | None

to_dict(refglues: set[str] = set()) → dict[str, Any]

class alhambra.tiles.DAOESingle(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: SingleTile, DAOETile

A tile with N, E, S and W edges.

class alhambra.tiles.DAOESingle5p(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: DAOESingle

A tile with N, E, S and W edges.

_baseglues: ClassVar[List[alhambra.glues.DXGlue]]

_gluelocs = [(0,), (3,), (3,), (0,)]

class alhambra.tiles.DAOESingle3p(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: DAOESingle

A tile with N, E, S and W edges.

_baseglues: ClassVar[List[alhambra.glues.DXGlue]]

_gluelocs = [(0,), (3,), (3,), (0,)]

class alhambra.tiles.DAOEHDouble3p(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: HDupleTile, DAOETile

Base class for a tile.

class alhambra.tiles.DAOEHDouble5p(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: HDupleTile, DAOETile

Base class for a tile.

class alhambra.tiles.DAOEVDouble3p(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: VDupleTile, DAOETile

Base class for a tile.

class alhambra.tiles.DAOEVDouble5p(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: VDupleTile, DAOETile

Base class for a tile.