alhambra.TileSet

class alhambra.TileSet(val={})

A class representing a single DNA tile assembly system.

This class parses and manipulates Alhambra tilesets. Note that, unless you have already imported or made a dict, you will likely want to construct this with TileSet.from_file.

Parameters:

val : dict

a dict in the Alhambra tileset format.

Attributes:

allends

All ends in the system, both from ends and tiles.

ends

The EndList of specified ends in the TileSet (not including ends that are only in tiles.

seed

Information on the tileset’s seed

strand_order_list

Return a list of orderable strand sequences for all tile strands.

tiles

Property returning the TileList of tiles in the TileSet

Methods

apply_equiv(equiv)	Apply an equivalence array (from, eg, TileSet.reduce_ends or TileSet.reduce_tiles).
check_consistent()	Check the TileSet consistency.
copy()	Return a full (deep) copy of the TileSet
create_abstract_diagrams(filename[, only_real])	Write abstract tile diagrams in SVG for the TileSet.
create_adapter_sequence_diagrams(filename, …)	Create sequence diagrams of adapters for the seed.
create_adapter_sequences()	Generate adapter sequences for the TileSet, returning a new TileSet with the generated sequences included.
create_end_sequences([method, energetics, …])	Create sticky end sequences for the TileSet, using stickydesign, and returning a new TileSet including the ends.
create_guard_strand_sequences()	Given a tileset dictionary with core tile sequences, create guard strand sequences.
create_layout_diagrams(xgrowarray, filename)	Create an SVG layout diagram from xgrow output.
create_sequence_diagrams(filename, *options)	Write sequence tile diagrams in SVG for the TileSet.
create_strand_sequences([basename, …])	Given a tileset dictionary with sticky ends sequences, create core sequences for tiles, using Pepper.
design_set([name, includes, energetics, …])	Helper function to design sets from scratch, calling the numerous parts of tilesetdesigner.
dump(stream)	Dump the tileset into a stream in YAML format.
from_file(name_or_stream, *args, **kwargs)	Class method to create a TileSet from a file or stream.
generate_xgrow_dict([perfect, rotate, …])	Generate a Xgrow tileset dict.
latticedefects([direction, depth, pp, rotate])	Calculate and show possible small lattice defect configurations.
plot_adjacent_regions([energetics])	Plots the strength of double-stranded regions in DX tiles adjacent to sticky ends.
plot_se_hists([all_energetics, …])	Plot histograms of sticky end energies, using stickydesign.plots.hist_multi.
plot_se_lv([all_energetics, …])	Uses an LV plot to show sticky end energetics.
plot_side_strands([energetics])	Plots the binding strength of short strands in DX tiles.
reduce_ends([preserve, tries, threads, …])	Apply end reduction algorithm, preserving some set of properties, and using a multiprocessing pool.
reduce_tiles([preserve, tries, threads, …])	Apply tile reduction algorithm, preserving some set of properties, and using a multiprocessing pool.
reorder_ends([newends, hightemp, lowtemp, …])	Given a tileset dictionary that includes sticky end sequences, reorder these to try to optimize error rates.
run_xgrow([xgrowparams, perfect, rotate, …])	Run Xgrow for the system.
summary()	Returns a short summary line about the TileSet
to_file(name_or_stream)	Write a TileSet to a file or stream.

__init__(val={})

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__([val])	Initialize self.
add_referent(cm)
add_yaml_merge(value)
apply_equiv(equiv)	Apply an equivalence array (from, eg, TileSet.reduce_ends or TileSet.reduce_tiles).
check_consistent()	Check the TileSet consistency.
clear()
copy()	Return a full (deep) copy of the TileSet
copy_attributes(t[, memo])
create_abstract_diagrams(filename[, only_real])	Write abstract tile diagrams in SVG for the TileSet.
create_adapter_sequence_diagrams(filename, …)	Create sequence diagrams of adapters for the seed.
create_adapter_sequences()	Generate adapter sequences for the TileSet, returning a new TileSet with the generated sequences included.
create_end_sequences([method, energetics, …])	Create sticky end sequences for the TileSet, using stickydesign, and returning a new TileSet including the ends.
create_guard_strand_sequences()	Given a tileset dictionary with core tile sequences, create guard strand sequences.
create_layout_diagrams(xgrowarray, filename)	Create an SVG layout diagram from xgrow output.
create_sequence_diagrams(filename, *options)	Write sequence tile diagrams in SVG for the TileSet.
create_strand_sequences([basename, …])	Given a tileset dictionary with sticky ends sequences, create core sequences for tiles, using Pepper.
design_set([name, includes, energetics, …])	Helper function to design sets from scratch, calling the numerous parts of tilesetdesigner.
dump(stream)	Dump the tileset into a stream in YAML format.
from_file(name_or_stream, *args, **kwargs)	Class method to create a TileSet from a file or stream.
fromkeys(/, iterable[, value])	Create a new ordered dictionary with keys from iterable and values set to value.
generate_xgrow_dict([perfect, rotate, …])	Generate a Xgrow tileset dict.
get(key[, default])	Return the value for key if key is in the dictionary, else default.
insert(pos, key, value[, comment])	insert key value into given position attach comment if provided
items()
keys()
latticedefects([direction, depth, pp, rotate])	Calculate and show possible small lattice defect configurations.
mlget(key[, default, list_ok])	multi-level get that expects dicts within dicts
move_to_end(/, key[, last])	Move an existing element to the end (or beginning if last is false).
non_merged_items()
plot_adjacent_regions([energetics])	Plots the strength of double-stranded regions in DX tiles adjacent to sticky ends.
plot_se_hists([all_energetics, …])	Plot histograms of sticky end energies, using stickydesign.plots.hist_multi.
plot_se_lv([all_energetics, …])	Uses an LV plot to show sticky end energetics.
plot_side_strands([energetics])	Plots the binding strength of short strands in DX tiles.
pop(k[,d])	value.
popitem(/[, last])	Remove and return a (key, value) pair from the dictionary.
reduce_ends([preserve, tries, threads, …])	Apply end reduction algorithm, preserving some set of properties, and using a multiprocessing pool.
reduce_tiles([preserve, tries, threads, …])	Apply tile reduction algorithm, preserving some set of properties, and using a multiprocessing pool.
reorder_ends([newends, hightemp, lowtemp, …])	Given a tileset dictionary that includes sticky end sequences, reorder these to try to optimize error rates.
run_xgrow([xgrowparams, perfect, rotate, …])	Run Xgrow for the system.
setdefault(/, key[, default])	Insert key with a value of default if key is not in the dictionary.
summary()	Returns a short summary line about the TileSet
to_file(name_or_stream)	Write a TileSet to a file or stream.
update([E, ]**F)	If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]
update_key_value(key)
values()
yaml_add_eol_comment(comment[, key, column])	there is a problem as eol comments should start with ‘ #’ (but at the beginning of the line the space doesn’t have to be before the #.
yaml_anchor()
yaml_end_comment_extend(comment[, clear])
yaml_key_comment_extend(key, comment[, clear])
yaml_set_anchor(value[, always_dump])
yaml_set_comment_before_after_key(key[, …])	expects comment (before/after) to be without # and possible have multiple lines
yaml_set_start_comment(comment[, indent])	overwrites any preceding comment lines on an object expects comment to be without # and possible have multiple lines
yaml_set_tag(value)
yaml_value_comment_extend(key, comment[, clear])

Attributes

allends	All ends in the system, both from ends and tiles.
anchor
ca
ends	The EndList of specified ends in the TileSet (not including ends that are only in tiles.
fa	format attribute
lc
merge
seed	Information on the tileset’s seed
strand_order_list	Return a list of orderable strand sequences for all tile strands.
tag
tiles	Property returning the TileList of tiles in the TileSet