RNAblueprint.h File Reference

This file holds the external representation of the DependencyGraph, the main construct for designing RNA molecules. More...

Go to the source code of this file.

Data Structures
class	design::DependencyGraph< R >
	Dependency Graph which holds all structural constraints. More...

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

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

Detailed Description

This file holds the external representation of the DependencyGraph, the main construct for designing RNA molecules.

The dependency graph is constructed from structures in dot-bracket notation and sequence constraints following the IUPAC notation. All important functions on the graph are available as member functions of this object.

Date

26.06.2014

Author

Stefan Hammer s.ham.nosp@m.mer@.nosp@m.univi.nosp@m.e.ac.nosp@m..at

Copyright

GPLv3

Definition in file RNAblueprint.h.