:py:mod:`alhambra._tilesets_dx`
===============================

.. py:module:: alhambra._tilesets_dx

.. autoapi-nested-parse::

   DX Tile TileSet routines.



Module Contents
---------------


Functions
~~~~~~~~~

.. autoapisummary::

   alhambra._tilesets_dx.stickydesign_create_dx_glue_sequences
   alhambra._tilesets_dx.dx_plot_se_hists
   alhambra._tilesets_dx.dx_plot_se_lv
   alhambra._tilesets_dx.dx_plot_adjacent_regions
   alhambra._tilesets_dx.dx_plot_side_strands



Attributes
~~~~~~~~~~

.. autoapisummary::

   alhambra._tilesets_dx.SELOGGER


.. py:data:: SELOGGER

   

.. py:function:: 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]]

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


   :param method: if 'default', use the default, single-model sequence design.
                  If 'multimodel', use multimodel end choice.
   :type method: {'default', 'multimodel'}
   :param 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.
   :type energetics: stickydesign.Energetics
   :param trials: the number of trials to attempt. FIXME
   :type trials: int
   :param sdopts: a dictionary of parameters to pass to stickydesign.easy_ends.
   :type sdopts: dict
   :param ecpars: a dictionary of parameters to pass to the endchooser function
                  generator (useful only in limited circumstances).
   :type ecpars: dict
   :param listends: if False, return just the TileSet.  If True, return both the
                    TileSet and a list of the names of the ends that were created.
   :type listends: bool

   :returns: * **tileset** (*TileSet*) -- TileSet with designed end sequences included.
             * **new_ends** (*list*) -- Names of the ends that were designed.


.. py:function:: 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

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

   :param all_energetics: A list of energetics to use.  Defaults to DEFAULT_MULTIMODEL_ENERGETICS.
   :type all_energetics: list of Energetics
   :param energetics_names: Names for energetics in all_energetics.  Defaults to DEFAULT_MM_ENERGETICS_NAMES.
   :type energetics_names: list of str
   :param title: Title for the plot.
   :type title: str
   :param \*\*kwargs: kwargs passed to stickydesign.plots.hist_multi.


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

   Uses an LV plot to show sticky end energetics.


.. py:function:: dx_plot_adjacent_regions(self: alhambra.tilesets.TileSet, energetics=None)

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

   :param energetics: The energetics to use.  Defaults to DEFAULT_REGION_ENERGETICS.
   :type energetics: stickydesign.Energetics


.. py:function:: dx_plot_side_strands(self: alhambra.tilesets.TileSet, energetics=None)

   Plots the binding strength of short strands in DX tiles.

   :param energetics: The energetics to use.  Defaults to DEFAULT_REGION_ENERGETICS.
   :type energetics: stickydesign.Energetics