design Namespace Reference

All classes and functions for the RNA design library are under the design namespace. More...

Data Structures
class	DependencyGraph
	Dependency Graph which holds all structural constraints. More...

Functions
void	initialize_library (bool debug)
	Initialize the Libraries global variables. More...
void	initialize_library (bool debug, int construction_timeout)
	Initialize the Libraries global variables. More...
std::string	structures_to_graphml (std::vector< std::string > structures, std::string constraints, bool decompose, unsigned long seed)
	Generate a graphml representation of structural and sequence constraints. More...
std::string	structures_to_graphml (std::vector< std::string > structures, std::string constraints, bool decompose)
	Generate a graphml representation of structural and sequence constraints. More...
std::string	structures_to_graphml (std::vector< std::string > structures, std::string constraints)
	Generate a graphml representation of structural and sequence constraints. More...
bool	graph_is_bipartite (std::vector< std::string > structures)
	Returns whether the dependency graph built from the given input structures is bipartite. More...
bool	sequence_structure_compatible (std::string sequence, std::vector< std::string > structures)
	Returns whether the the given sequence is compatible to all the given structures. More...
std::vector< int >	incompatible_sequence_positions (std::string sequence, std::string structure)
	Returns whether the the given sequence is compatible to all the given structures. More...

Detailed Description

All classes and functions for the RNA design library are under the design namespace.

Function Documentation

graph_is_bipartite()

bool design::graph_is_bipartite

(

std::vector< std::string >

structures

)

Returns whether the dependency graph built from the given input structures is bipartite.

This helper function checks, if a set of input structures will generate a bipartite dependency graph. If the graph is not bipartite, it cannot be used to generate a valid RNA sequence.

Parameters

structures

vector of string structures in dot-bracket notation.

Exceptions

std::exception

if input is invalid or construction fails an exception is thrown.

Returns

boolean specifying whether the input structures can be constructed to a bipartite dependency graph.

incompatible_sequence_positions()

std::vector<int> design::incompatible_sequence_positions	(	std::string	sequence,
		std::string	structure
	)

Returns whether the the given sequence is compatible to all the given structures.

This function checks, if a given sequence can fold into the given structure and returns an empty vector if this is the case. Else, it returns all positions on the sequence which are incompatible with the given structural constraint. E.g. incompatible_sequence_positions("ANC", "(.)") would return [0, 2]!

Parameters

sequence	string in IUPAC notation.
structure	string in dot-bracket notation.

Exceptions

std::exception

if input is invalid.

Returns

map of a pair of integers specifying the sequence positions incompatible to the structure input.

initialize_library() [1/2]

void design::initialize_library

(

bool

debug

)

Initialize the Libraries global variables.

Parameters

debug

boolean whether to print debugging information to std:err (default: false)

initialize_library() [2/2]

void design::initialize_library	(	bool	debug,
		int	construction_timeout
	)

Initialize the Libraries global variables.

Parameters

debug	boolean whether to print debugging information to std:err (default: false)
construction_timeout	integer specifying the dependency graph construction timeout in seconds. 0 is infinite. (default: 0)

sequence_structure_compatible()

bool design::sequence_structure_compatible	(	std::string	sequence,
		std::vector< std::string >	structures
	)

Returns whether the the given sequence is compatible to all the given structures.

This function checks, if a given sequence can form all base-pairs given by a set of input structures. Or the other way around, if the given structures could have produced this sequence.

Parameters

sequence	string in IUPAC notation.
structures	vector of string structures in dot-bracket notation.

Exceptions

std::exception

if input is invalid.

Returns

boolean specifying whether the input sequence is compatible to all the given structures.

structures_to_graphml() [1/3]

std::string design::structures_to_graphml	(	std::vector< std::string >	structures,
		std::string	constraints
	)

Generate a graphml representation of structural and sequence constraints.

This function generates a graphml representation of the dependency graph given some structural and sequence constraints without constructing a DependencyGraph object, but with decomposition of the graph into subpaths. It is mainly thought to be useful for developmental purposes, analysis of hard problems and vizualisation.

Parameters

structures	vector of string structures in dot-bracket notation.
constraints	string containing the sequence constraints in IUPAC notation. Can also be a empty string!

Exceptions

std::exception

if input is invalid or construction/decomposition fails an exception is thrown.

Returns

string containing the GraphML notation of the dependency graph.

structures_to_graphml() [2/3]

std::string design::structures_to_graphml	(	std::vector< std::string >	structures,
		std::string	constraints,
		bool	decompose
	)

Generate a graphml representation of structural and sequence constraints.

This function generates a graphml representation of the dependency graph given some structural and sequence constraints without constructing a DependencyGraph object, with or without decomposition of the graph into subpaths. It is mainly thought to be useful for developmental purposes, analysis of hard problems and vizualisation. Caution: There are random parts in the decomposition algorithms. If you want to assign a seed, use structures_to_graphml(std::vector<std::string> structures, std::string constraints, bool decompose, unsigned long seed)

Parameters

structures	vector of string structures in dot-bracket notation.
constraints	string containing the sequence constraints in IUPAC notation. Can also be a empty string!
decompose	boolean Whether to decompose the dependency graph into paths and therefore draw articulation vertices and ears.

Exceptions

std::exception

if input is invalid or construction/decomposition fails an exception is thrown.

Returns

string containing the GraphML notation of the dependency graph.

structures_to_graphml() [3/3]

std::string design::structures_to_graphml	(	std::vector< std::string >	structures,
		std::string	constraints,
		bool	decompose,
		unsigned long	seed
	)

Generate a graphml representation of structural and sequence constraints.

This function generates a graphml representation of the dependency graph given some structural and sequence constraints without constructing a DependencyGraph object, with or without decomposition of the graph into subpaths. It is mainly thought to be useful for developmental purposes, analysis of hard problems and vizualisation.

Parameters

structures	vector of string structures in dot-bracket notation.
constraints	string containing the sequence constraints in IUPAC notation. Can also be a empty string!
decompose	boolean Whether to decompose the dependency graph into paths and therefore draw articulation vertices and ears.
seed	unsigned long Seed for the random number generator which is used for some random parts of the decomposition.

Exceptions

std::exception

if input is invalid or construction/decomposition fails an exception is thrown.

Returns

string containing the GraphML notation of the dependency graph.