API for various RNA folding path algorithms. More...

Detailed Description

API for various RNA folding path algorithms.

This part of our API allows for generating RNA secondary structure (re-)folding paths between two secondary structures or simply starting from a single structure. This is most important if an estimate of the refolding energy barrier between two structures is required, or a structure's corresponding local minimum needs to be determined, e.g. through a gradient-descent walk.

This part of the interface is further split into the following sections:

Collaboration diagram for (Re-)folding Paths, Saddle Points, Energy Barriers, and Local Minima:

Modules
	Direct Refolding Paths between two Secondary Structures
	Heuristics to explore direct, optimal (re-)folding paths between two secondary structures.

	Folding Paths that start at a single Secondary Structure
	Implementation of gradient- and random walks starting from a single secondary structure.

	Deprecated Interface for (Re-)folding Paths, Saddle Points, and Energy Barriers

Files
file	findpath.h
	A breadth-first search heuristic for optimal direct folding paths.

file	paths.h
	API for computing (optimal) (re-)folding paths between secondary structures.

file	walk.h
	Methods to generate particular paths such as gradient or random walks through the energy landscape of an RNA sequence.

Data Structures
struct	vrna_path_s
	An element of a refolding path list. More...

Macros
#define	VRNA_PATH_TYPE_DOT_BRACKET 1U
	Flag to indicate producing a (re-)folding path as list of dot-bracket structures. More...

#define	VRNA_PATH_TYPE_MOVES 2U
	Flag to indicate producing a (re-)folding path as list of transition moves. More...

Typedefs
typedef struct vrna_path_s	vrna_path_t
	Typename for the refolding path data structure vrna_path_s.

typedef struct vrna_path_options_s *	vrna_path_options_t
	Options data structure for (re-)folding path implementations.

Functions
void	vrna_path_free (vrna_path_t *path)
	Release (free) memory occupied by a (re-)folding path. More...

void	vrna_path_options_free (vrna_path_options_t options)
	Release (free) memory occupied by an options data structure for (re-)folding path implementations. More...

Data Structure Documentation

struct vrna_path_s

An element of a refolding path list.

Usually, one has to deal with an array of vrna_path_s, e.g. returned from one of the refolding-path algorithms.

Since in most cases the length of the list is not known in advance, such lists have an end-of-list marker, which is either:

a value of NULL for vrna_path_s::s if vrna_path_s::type = VRNA_PATH_TYPE_DOT_BRACKET, or
a vrna_path_s::move with zero in both fields vrna_move_t::pos_5 and vrna_move_t::pos_3 if vrna_path_s::type = VRNA_PATH_TYPE_MOVES.

In the following we show an example for how to cover both cases of iteration:

vrna_path_t *ptr = path; // path was returned from one of the refolding path functions, e.g. vrna_path_direct()
if (ptr) {
  if (ptr->type == VRNA_PATH_TYPE_DOT_BRACKET) {
    for (; ptr->s; ptr++)
      printf("%s [%6.2f]\n", ptr->s, ptr->en);
  } else if (ptr->type == VRNA_PATH_TYPE_MOVES) {
    for (; ptr->move.pos_5 != 0; ptr++)
      printf("move %d:%d, dG = %6.2f\n", ptr->move.pos_5, ptr->move.pos_3, ptr->en);
  }
}

See also: vrna_path_free()

Collaboration diagram for vrna_path_s:

Data Fields
unsigned int	type
	The type of the path element. More...

double	en
	Free energy of current structure.

char *	s
	Secondary structure in dot-bracket notation.

vrna_move_t	move
	Move that transforms the previous structure into it's next neighbor along the path.

Field Documentation

unsigned int vrna_path_s::type

The type of the path element.

A value of VRNA_PATH_TYPE_DOT_BRACKET indicates that vrna_path_s::s consists of the secondary structure in dot-bracket notation, and vrna_path_s::en the corresponding free energy.
On the other hand, if the value is VRNA_PATH_TYPE_MOVES, vrna_path_s::s is NULL and vrna_path_s::move is set to the transition move that transforms a previous structure into it's neighbor along the path. In this case, the attribute vrna_path_s::en states the change in free energy with respect to the structure before application of vrna_path_s::move.