Heuristics to explore direct, optimal (re-)folding paths between two secondary structures. More...

Detailed Description

Heuristics to explore direct, optimal (re-)folding paths between two secondary structures.

Collaboration diagram for Direct Refolding Paths between two Secondary Structures:

Functions
int	vrna_path_findpath_saddle (vrna_fold_compound_t fc, const char s1, const char *s2, int width)
	Find energy of a saddle point between 2 structures (search only direct path) More...

int	vrna_path_findpath_saddle_ub (vrna_fold_compound_t fc, const char s1, const char *s2, int width, int maxE)
	Find energy of a saddle point between 2 structures (search only direct path) More...

vrna_path_t *	vrna_path_findpath (vrna_fold_compound_t fc, const char s1, const char *s2, int width)
	Find refolding path between 2 structures (search only direct path) More...

vrna_path_t *	vrna_path_findpath_ub (vrna_fold_compound_t fc, const char s1, const char *s2, int width, int maxE)
	Find refolding path between 2 structures (search only direct path) More...

vrna_path_options_t	vrna_path_options_findpath (int width, unsigned int type)
	Create options data structure for findpath direct (re-)folding path heuristic. More...

vrna_path_t *	vrna_path_direct (vrna_fold_compound_t fc, const char s1, const char *s2, vrna_path_options_t options)
	Determine an optimal direct (re-)folding path between two secondary structures. More...

vrna_path_t *	vrna_path_direct_ub (vrna_fold_compound_t fc, const char s1, const char *s2, int maxE, vrna_path_options_t options)
	Determine an optimal direct (re-)folding path between two secondary structures. More...

Function Documentation

int vrna_path_findpath_saddle	(	vrna_fold_compound_t *	vc,
		const char *	s1,
		const char *	s2,
		int	width
	)

#include <ViennaRNA/landscape/findpath.h>

Find energy of a saddle point between 2 structures (search only direct path)

This function uses an inplementation of the findpath algorithm [7] for near-optimal direct refolding path prediction.

Model details, and energy parameters are used as provided via the parameter 'fc'. The vrna_fold_compound_t does not require memory for any DP matrices, but requires all most basic init values as one would get from a call like this:

fc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_DEFAULT);

See also: vrna_path_findpath_saddle_ub(), vrna_fold_compound(), vrna_fold_compound_t, vrna_path_findpath()

Parameters

fc	The vrna_fold_compound_t with precomputed sequence encoding and model details
s1	The start structure in dot-bracket notation
s2	The target structure in dot-bracket notation
width	A number specifying how many strutures are being kept at each step during the search

Returns: The saddle energy in 10cal/mol

SWIG Wrapper Notes:: This function is attached as an overloaded method path_findpath_saddle() to objects of type fold_compound. The optional parameter width defaults to 1 if it is omitted.

int vrna_path_findpath_saddle_ub	(	vrna_fold_compound_t *	vc,
		const char *	s1,
		const char *	s2,
		int	width,
		int	maxE
	)

#include <ViennaRNA/landscape/findpath.h>

Find energy of a saddle point between 2 structures (search only direct path)

This function uses an inplementation of the findpath algorithm [7] for near-optimal direct refolding path prediction.

Model details, and energy parameters are used as provided via the parameter 'fc'. The vrna_fold_compound_t does not require memory for any DP matrices, but requires all most basic init values as one would get from a call like this:

fc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_DEFAULT);

Warning: The argument maxE ( $E_{max}$ ) enables one to specify an upper bound, or maximum free energy for the saddle point between the two input structures. If no path with $E_{saddle} < E_{max}$ is found, the function simply returns maxE

See also: vrna_path_findpath_saddle(), vrna_fold_compound(), vrna_fold_compound_t, vrna_path_findpath()

Parameters

fc	The vrna_fold_compound_t with precomputed sequence encoding and model details
s1	The start structure in dot-bracket notation
s2	The target structure in dot-bracket notation
width	A number specifying how many strutures are being kept at each step during the search
maxE	An upper bound for the saddle point energy in 10cal/mol

Returns: The saddle energy in 10cal/mol

SWIG Wrapper Notes:: This function is attached as an overloaded method path_findpath_saddle() to objects of type fold_compound. The optional parameter width defaults to 1 if it is omitted, while the optional parameter maxE defaults to INF. In case the function did not find a path with $E_{saddle} < E_{max}$ the function returns a NULL object, i.e. undef for Perl and None for Python.

vrna_path_t * vrna_path_findpath	(	vrna_fold_compound_t *	vc,
		const char *	s1,
		const char *	s2,
		int	width
	)

#include <ViennaRNA/landscape/findpath.h>

Find refolding path between 2 structures (search only direct path)

This function uses an inplementation of the findpath algorithm [7] for near-optimal direct refolding path prediction.

Model details, and energy parameters are used as provided via the parameter 'fc'. The vrna_fold_compound_t does not require memory for any DP matrices, but requires all most basic init values as one would get from a call like this:

fc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_DEFAULT);

See also: vrna_path_findpath_ub(), vrna_fold_compound(), vrna_fold_compound_t, vrna_path_findpath_saddle()

Parameters

fc	The vrna_fold_compound_t with precomputed sequence encoding and model details
s1	The start structure in dot-bracket notation
s2	The target structure in dot-bracket notation
width	A number specifying how many strutures are being kept at each step during the search

Returns: The saddle energy in 10cal/mol

SWIG Wrapper Notes:: This function is attached as an overloaded method path_findpath() to objects of type fold_compound. The optional parameter width defaults to 1 if it is omitted.

vrna_path_t * vrna_path_findpath_ub	(	vrna_fold_compound_t *	vc,
		const char *	s1,
		const char *	s2,
		int	width,
		int	maxE
	)

#include <ViennaRNA/landscape/findpath.h>

Find refolding path between 2 structures (search only direct path)

This function uses an inplementation of the findpath algorithm [7] for near-optimal direct refolding path prediction.

Model details, and energy parameters are used as provided via the parameter 'fc'. The vrna_fold_compound_t does not require memory for any DP matrices, but requires all most basic init values as one would get from a call like this:

fc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_DEFAULT);

Warning: The argument maxE enables one to specify an upper bound, or maximum free energy for the saddle point between the two input structures. If no path with $E_{saddle} < E_{max}$ is found, the function simply returns NULL

See also: vrna_path_findpath(), vrna_fold_compound(), vrna_fold_compound_t, vrna_path_findpath_saddle()

Parameters

fc	The vrna_fold_compound_t with precomputed sequence encoding and model details
s1	The start structure in dot-bracket notation
s2	The target structure in dot-bracket notation
width	A number specifying how many strutures are being kept at each step during the search
maxE	An upper bound for the saddle point energy in 10cal/mol

Returns: The saddle energy in 10cal/mol

SWIG Wrapper Notes:: This function is attached as an overloaded method path_findpath() to objects of type fold_compound. The optional parameter width defaults to 1 if it is omitted, while the optional parameter maxE defaults to INF. In case the function did not find a path with $E_{saddle} < E_{max}$ the function returns an empty list.

vrna_path_options_t vrna_path_options_findpath	(	int	width,
		unsigned int	type
	)

#include <ViennaRNA/landscape/paths.h>

Create options data structure for findpath direct (re-)folding path heuristic.

This function returns an options data structure that switches the vrna_path_direct() and vrna_path_direct_ub() API functions to use the findpath [7] heuristic. The parameter width specifies the width of the breadth-first search while the second parameter type allows one to set the type of the returned (re-)folding path.

Currently, the following return types are available:

A list of dot-bracket structures and corresponding free energy (flag: VRNA_PATH_TYPE_DOT_BRACKET)
A list of transition moves and corresponding free energy changes (flag: VRNA_PATH_TYPE_MOVES)

See also: VRNA_PATH_TYPE_DOT_BRACKET, VRNA_PATH_TYPE_MOVES, vrna_path_options_free(), vrna_path_direct(), vrna_path_direct_ub()

Parameters

width	Width of the breath-first search strategy
type	Setting that specifies how the return (re-)folding path should be encoded

Returns: An options data structure with settings for the findpath direct path heuristic

SWIG Wrapper Notes:: This function is available as overloaded function path_options_findpath(). The optional parameter width defaults to 10 if omitted, while the optional parameter type defaults to VRNA_PATH_TYPE_DOT_BRACKET.

vrna_path_t * vrna_path_direct	(	vrna_fold_compound_t *	fc,
		const char *	s1,
		const char *	s2,
		vrna_path_options_t	options
	)

#include <ViennaRNA/landscape/paths.h>

Determine an optimal direct (re-)folding path between two secondary structures.

This is the generic wrapper function to retrieve (an optimal) (re-)folding path between two secondary structures s1 and s2. The actual algorithm that is used to generate the (re-)folding path is determined by the settings specified in the options data structure. This data structure also determines the return type, which might be either:

a list of dot-bracket structures with corresponding free energy, or
a list of transition moves with corresponding free energy change

If the options parameter is passed a NULL pointer, this function defaults to the findpath heuristic [7] with a breadth-first search width of $ 10 $ , and the returned path consists of dot-bracket structures with corresponding free energies.

See also: vrna_path_direct_ub(), vrna_path_options_findpath(), vrna_path_options_free(), vrna_path_free()

Parameters

fc	The vrna_fold_compound_t with precomputed sequence encoding and model details
s1	The start structure in dot-bracket notation
s2	The target structure in dot-bracket notation
options	An options data structure that specifies the path heuristic and corresponding settings (maybe NULL)

Returns: An optimal (re-)folding path between the two input structures

SWIG Wrapper Notes:: This function is attached as an overloaded method path_direct() to objects of type fold_compound. The optional parameter options defaults to NULL if it is omitted.

vrna_path_t * vrna_path_direct_ub	(	vrna_fold_compound_t *	fc,
		const char *	s1,
		const char *	s2,
		int	maxE,
		vrna_path_options_t	options
	)

#include <ViennaRNA/landscape/paths.h>

Determine an optimal direct (re-)folding path between two secondary structures.

This function is similar to vrna_path_direct(), but allows to specify an upper-bound for the saddle point energy. The underlying algorithms will stop determining an (optimal) (re-)folding path, if none can be found that has a saddle point below the specified upper-bound threshold maxE.

Warning: The argument maxE enables one to specify an upper bound, or maximum free energy for the saddle point between the two input structures. If no path with $E_{saddle} < E_{max}$ is found, the function simply returns NULL

See also: vrna_path_direct_ub(), vrna_path_options_findpath(), vrna_path_options_free(), vrna_path_free()

Parameters

fc	The vrna_fold_compound_t with precomputed sequence encoding and model details
s1	The start structure in dot-bracket notation
s2	The target structure in dot-bracket notation
maxE	Upper bound for the saddle point along the (re-)folding path
options	An options data structure that specifies the path heuristic and corresponding settings (maybe NULL)

Returns: An optimal (re-)folding path between the two input structures

SWIG Wrapper Notes:: This function is attached as an overloaded method path_direct() to objects of type fold_compound. The optional parameter maxE defaults to #INT_MAX - 1 if it is omitted, while the optional parameter options defaults to NULL. In case the function did not find a path with $E_{saddle} < E_{max}$ it returns an empty list.

Detailed Description

Functions

Function Documentation