RNAblueprint-1.3.2
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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... | |
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.
Definition in file RNAblueprint.h.