Implementation of gradient- and random walks starting from a single secondary structure. More...

Detailed Description

Implementation of gradient- and random walks starting from a single secondary structure.

Collaboration diagram for Folding Paths that start at a single Secondary Structure:

Macros
#define	VRNA_PATH_STEEPEST_DESCENT 128
	Option flag to request a steepest descent / gradient path. More...

#define	VRNA_PATH_RANDOM 256
	Option flag to request a random walk path. More...

#define	VRNA_PATH_NO_TRANSITION_OUTPUT 512
	Option flag to omit returning the transition path. More...

#define	VRNA_PATH_DEFAULT (VRNA_PATH_STEEPEST_DESCENT \| VRNA_MOVESET_DEFAULT)
	Option flag to request defaults (steepest descent / default move set) More...

Functions
vrna_move_t *	vrna_path (vrna_fold_compound_t vc, short pt, unsigned int steps, unsigned int options)
	Compute a path, store the final structure, and return a list of transition moves from the start to the final structure. More...

vrna_move_t *	vrna_path_gradient (vrna_fold_compound_t vc, short pt, unsigned int options)
	Compute a steepest descent / gradient path, store the final structure, and return a list of transition moves from the start to the final structure. More...

vrna_move_t *	vrna_path_random (vrna_fold_compound_t vc, short pt, unsigned int steps, unsigned int options)
	Generate a random walk / path of a given length, store the final structure, and return a list of transition moves from the start to the final structure. More...

Macro Definition Documentation

#define VRNA_PATH_STEEPEST_DESCENT 128

#include <ViennaRNA/landscape/walk.h>

Option flag to request a steepest descent / gradient path.

See also: vrna_path()

#define VRNA_PATH_RANDOM 256

#include <ViennaRNA/landscape/walk.h>

Option flag to request a random walk path.

See also: vrna_path()

#define VRNA_PATH_NO_TRANSITION_OUTPUT 512

#include <ViennaRNA/landscape/walk.h>

Option flag to omit returning the transition path.

See also: vrna_path(), vrna_path_gradient(), vrna_path_random()

#define VRNA_PATH_DEFAULT (VRNA_PATH_STEEPEST_DESCENT | VRNA_MOVESET_DEFAULT)

#include <ViennaRNA/landscape/walk.h>

Option flag to request defaults (steepest descent / default move set)

See also: vrna_path(), VRNA_PATH_STEEPEST_DESCENT, VRNA_MOVESET_DEFAULT

Function Documentation

vrna_move_t * vrna_path	(	vrna_fold_compound_t *	vc,
		short *	pt,
		unsigned int	steps,
		unsigned int	options
	)

#include <ViennaRNA/landscape/walk.h>

Compute a path, store the final structure, and return a list of transition moves from the start to the final structure.

This function computes, given a start structure in pair table format, a transition path, updates the pair table to the final structure of the path. Finally, if not requested otherwise by using the VRNA_PATH_NO_TRANSITION_OUTPUT flag in the options field, this function returns a list of individual transitions that lead from the start to the final structure if requested.

The currently available transition paths are

Steepest Descent / Gradient walk (flag: VRNA_PATH_STEEPEST_DESCENT)
Random walk (flag: VRNA_PATH_RANDOM)

The type of transitions must be set through the options parameter

Note: Since the result is written to the input structure you may want to use vrna_ptable_copy() before calling this function to keep the initial structure

See also: vrna_path_gradient(), vrna_path_random(), vrna_ptable(), vrna_ptable_copy(), vrna_fold_compound() VRNA_PATH_STEEPEST_DESCENT, VRNA_PATH_RANDOM, VRNA_MOVESET_DEFAULT, VRNA_MOVESET_SHIFT, VRNA_PATH_NO_TRANSITION_OUTPUT

Parameters

[in]	vc	A vrna_fold_compound_t containing the energy parameters and model details
[in,out]	pt	The pair table containing the start structure. Used to update to the final structure after execution of this function
[in]	options	Options to modify the behavior of this function

Returns: A list of transition moves (default), or NULL (if options & VRNA_PATH_NO_TRANSITION_OUTPUT)

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

vrna_move_t * vrna_path_gradient	(	vrna_fold_compound_t *	vc,
		short *	pt,
		unsigned int	options
	)

#include <ViennaRNA/landscape/walk.h>

Compute a steepest descent / gradient path, store the final structure, and return a list of transition moves from the start to the final structure.

This function computes, given a start structure in pair table format, a steepest descent path, updates the pair table to the final structure of the path. Finally, if not requested otherwise by using the VRNA_PATH_NO_TRANSITION_OUTPUT flag in the options field, this function returns a list of individual transitions that lead from the start to the final structure if requested.

Note: Since the result is written to the input structure you may want to use vrna_ptable_copy() before calling this function to keep the initial structure

See also: vrna_path_random(), vrna_path(), vrna_ptable(), vrna_ptable_copy(), vrna_fold_compound() VRNA_MOVESET_DEFAULT, VRNA_MOVESET_SHIFT, VRNA_PATH_NO_TRANSITION_OUTPUT

Parameters

[in]	vc	A vrna_fold_compound_t containing the energy parameters and model details
[in,out]	pt	The pair table containing the start structure. Used to update to the final structure after execution of this function
[in]	options	Options to modify the behavior of this function

Returns: A list of transition moves (default), or NULL (if options & VRNA_PATH_NO_TRANSITION_OUTPUT)

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

vrna_move_t * vrna_path_random	(	vrna_fold_compound_t *	vc,
		short *	pt,
		unsigned int	steps,
		unsigned int	options
	)

#include <ViennaRNA/landscape/walk.h>

Generate a random walk / path of a given length, store the final structure, and return a list of transition moves from the start to the final structure.

This function generates, given a start structure in pair table format, a random walk / path, updates the pair table to the final structure of the path. Finally, if not requested otherwise by using the VRNA_PATH_NO_TRANSITION_OUTPUT flag in the options field, this function returns a list of individual transitions that lead from the start to the final structure if requested.

Note: Since the result is written to the input structure you may want to use vrna_ptable_copy() before calling this function to keep the initial structure

See also: vrna_path_gradient(), vrna_path(), vrna_ptable(), vrna_ptable_copy(), vrna_fold_compound() VRNA_MOVESET_DEFAULT, VRNA_MOVESET_SHIFT, VRNA_PATH_NO_TRANSITION_OUTPUT

Parameters

[in]	vc	A vrna_fold_compound_t containing the energy parameters and model details
[in,out]	pt	The pair table containing the start structure. Used to update to the final structure after execution of this function
[in]	steps	The length of the path, i.e. the total number of transitions / moves
[in]	options	Options to modify the behavior of this function

Returns: A list of transition moves (default), or NULL (if options & VRNA_PATH_NO_TRANSITION_OUTPUT)

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

Detailed Description

Macros

Functions

Macro Definition Documentation

Function Documentation