RNAblueprint-1.3.2
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

Definition in file RNAblueprint.h.