alhambra._tilesets_dx#

DX Tile TileSet routines.

Module Contents#

Functions#

stickydesign_create_dx_glue_sequences(...)

Create sticky end sequences for the TileSet, using stickydesign,

dx_plot_se_hists(→ Any)

Plot histograms of sticky end energies, using stickydesign.plots.hist_multi.

dx_plot_se_lv(self[, all_energetics, ...])

Uses an LV plot to show sticky end energetics.

dx_plot_adjacent_regions(self[, energetics])

Plots the strength of double-stranded regions in DX tiles adjacent

dx_plot_side_strands(self[, energetics])

Plots the binding strength of short strands in DX tiles.

Attributes#

SELOGGER

alhambra._tilesets_dx.SELOGGER[source]#
alhambra._tilesets_dx.stickydesign_create_dx_glue_sequences(self, method: Literal[default, stickydesign.multimodel] = 'default', energetics: stickydesign.Energetics | None = None, trials: int = 100, devmethod='dev', sdopts: dict[str, Any] | None = None, ecpars: dict[str, Any] | None = None, listends: bool = False) → tuple[alhambra.tilesets.TileSet, Sequence[str]][source]#

Create sticky end sequences for the TileSet, using stickydesign, and returning a new TileSet including the ends.

Parameters:

  • method ({'default', 'multimodel'}) – if ‘default’, use the default, single-model sequence design. If ‘multimodel’, use multimodel end choice.

  • energetics (stickydesign.Energetics) – the energetics instance to use for the design, or list of energetics for method=’multimodel’, in which case the first will be the primary. If None (default), will use alhambra.DEFAULT_ENERGETICS, or, if method=’multimodel’, will use alhambra.DEFAULT_MM_ENERGETICS.

  • trials (int) – the number of trials to attempt. FIXME

  • sdopts (dict) – a dictionary of parameters to pass to stickydesign.easy_ends.

  • ecpars (dict) – a dictionary of parameters to pass to the endchooser function generator (useful only in limited circumstances).

  • listends (bool) – if False, return just the TileSet. If True, return both the TileSet and a list of the names of the ends that were created.

Returns:

  • tileset (TileSet) – TileSet with designed end sequences included.

  • new_ends (list) – Names of the ends that were designed.

alhambra._tilesets_dx.dx_plot_se_hists(self: alhambra.tilesets.TileSet, all_energetics: Sequence[stickydesign.Energetics] | None = None, energetics_names: Sequence[str] | None = None, title: str | None = None, **kwargs: Any) → Any[source]#

Plot histograms of sticky end energies, using stickydesign.plots.hist_multi.

Parameters:

  • all_energetics (list of Energetics) – A list of energetics to use. Defaults to DEFAULT_MULTIMODEL_ENERGETICS.

  • energetics_names (list of str) – Names for energetics in all_energetics. Defaults to DEFAULT_MM_ENERGETICS_NAMES.

  • title (str) – Title for the plot.

  • **kwargs – kwargs passed to stickydesign.plots.hist_multi.

alhambra._tilesets_dx.dx_plot_se_lv(self: alhambra.tilesets.TileSet, all_energetics: Sequence[stickydesign.Energetics] | None = None, energetics_names: Sequence[str] | None = None, pltcmd: Callable[[Any], Any] | None = None, title: str | None = None, **kwargs)[source]#

Uses an LV plot to show sticky end energetics.

alhambra._tilesets_dx.dx_plot_adjacent_regions(self: alhambra.tilesets.TileSet, energetics=None)[source]#

Plots the strength of double-stranded regions in DX tiles adjacent to sticky ends.

Parameters:

energetics (stickydesign.Energetics) – The energetics to use. Defaults to DEFAULT_REGION_ENERGETICS.

alhambra._tilesets_dx.dx_plot_side_strands(self: alhambra.tilesets.TileSet, energetics=None)[source]#

Plots the binding strength of short strands in DX tiles.

Parameters:

energetics (stickydesign.Energetics) – The energetics to use. Defaults to DEFAULT_REGION_ENERGETICS.