Suboptimal Structures within an Energy Band around the MFE

Detailed Description

Collaboration diagram for Suboptimal Structures within an Energy Band around the MFE:

Typedefs
typedef void(	vrna_subopt_callback) (const char *stucture, float energy, void *data)
	Callback for vrna_subopt_cb() More...

Functions
vrna_subopt_solution_t *	vrna_subopt (vrna_fold_compound_t *vc, int delta, int sorted, FILE *fp)
	Returns list of subopt structures or writes to fp. More...
void	vrna_subopt_cb (vrna_fold_compound_t *vc, int delta, vrna_subopt_callback *cb, void *data)
	Generate suboptimal structures within an energy band arround the MFE. More...
SOLUTION *	subopt (char *seq, char *structure, int delta, FILE *fp)
	Returns list of subopt structures or writes to fp. More...
SOLUTION *	subopt_par (char *seq, char *structure, vrna_param_t *parameters, int delta, int is_constrained, int is_circular, FILE *fp)
	Returns list of subopt structures or writes to fp.
SOLUTION *	subopt_circ (char *seq, char *sequence, int delta, FILE *fp)
	Returns list of circular subopt structures or writes to fp. More...

Variables
double	print_energy
	printing threshold for use with logML
int	subopt_sorted
	Sort output by energy.

Typedef Documentation

typedef void( vrna_subopt_callback) (const char *stucture, float energy, void *data)

#include <ViennaRNA/subopt.h>

Callback for vrna_subopt_cb()

Notes on Callback Functions:

This function will be called for each suboptimal secondary structure that is successfully backtraced.

See also

vrna_subopt_cb()

Parameters

structure	The suboptimal secondary structure in dot-bracket notation
energy	The free energy of the secondary structure in kcal/mol
data	Some arbitrary, auxiliary data address as passed to vrna_subopt_cb()

Function Documentation

vrna_subopt_solution_t * vrna_subopt	(	vrna_fold_compound_t *	vc,
		int	delta,
		int	sorted,
		FILE *	fp
	)

#include <ViennaRNA/subopt.h>

Returns list of subopt structures or writes to fp.

This function produces all suboptimal secondary structures within 'delta' * 0.01 kcal/mol of the optimum, see [24]. The results are either directly written to a 'fp' (if 'fp' is not NULL), or (fp==NULL) returned in a vrna_subopt_solution_t * list terminated by an entry were the 'structure' member is NULL.

Note

This function requires all multibranch loop DP matrices for unique multibranch loop backtracing. Therefore, the supplied vrna_fold_compound_t vc (argument 1) must be initialized with vrna_md_t.uniq_ML = 1, for instance like this:

vrna_md_t md;
vrna_md_set_default(&md);
md.uniq_ML = 1;

vrna_fold_compound_t *vc=vrna_fold_compound("GGGGGGAAAAAACCCCCC", &md, VRNA_OPTION_DEFAULT);

See also

vrna_subopt_cb(), vrna_subopt_zuker()

Parameters

vc
delta
sorted	Sort results by energy in ascending order
fp

Returns

SWIG Wrapper Notes:

This function is attached as method subopt() to objects of type fold_compound

void vrna_subopt_cb	(	vrna_fold_compound_t *	vc,
		int	delta,
		vrna_subopt_callback *	cb,
		void *	data
	)

#include <ViennaRNA/subopt.h>

Generate suboptimal structures within an energy band arround the MFE.

This is the most generic implementation of the suboptimal structure generator according to Wuchty et al. 1999 [24]. Identical to vrna_subopt(), it computes all secondary structures within an energy band delta arround the MFE. However, this function does not print the resulting structures and their corresponding free energies to a file pointer, or returns them as a list. Instead, it calls a user-provided callback function which it passes the structure in dot-bracket format, the corresponding free energy in kcal/mol, and a user-provided data structure each time a structure was backtracked successfully. This function indicates the final output, i.e. the end of the backtracking procedure by passing NULL instead of an actual dot-bracket string to the callback.

Note

This function requires all multibranch loop DP matrices for unique multibranch loop backtracing. Therefore, the supplied vrna_fold_compound_t vc (argument 1) must be initialized with vrna_md_t.uniq_ML = 1, for instance like this:

vrna_md_t md;
vrna_md_set_default(&md);
md.uniq_ML = 1;

vrna_fold_compound_t *vc=vrna_fold_compound("GGGGGGAAAAAACCCCCC", &md, VRNA_OPTION_DEFAULT);

See also

vrna_subopt_callback, vrna_subopt(), vrna_subopt_zuker()

Parameters

vc	fold compount with the sequence data
delta	Energy band arround the MFE in 10cal/mol, i.e. deka-calories
cb	Pointer to a callback function that handles the backtracked structure and its free energy in kcal/mol
data	Pointer to some data structure that is passed along to the callback

SWIG Wrapper Notes:

This function is attached as method subopt_cb() to objects of type fold_compound

SOLUTION* subopt	(	char *	seq,
		char *	structure,
		int	delta,
		FILE *	fp
	)

#include <ViennaRNA/subopt.h>

Returns list of subopt structures or writes to fp.

This function produces all suboptimal secondary structures within 'delta' * 0.01 kcal/mol of the optimum. The results are either directly written to a 'fp' (if 'fp' is not NULL), or (fp==NULL) returned in a SOLUTION * list terminated by an entry were the 'structure' pointer is NULL.

Parameters

seq
structure
delta
fp

Returns

SOLUTION* subopt_circ	(	char *	seq,
		char *	sequence,
		int	delta,
		FILE *	fp
	)

#include <ViennaRNA/subopt.h>

Returns list of circular subopt structures or writes to fp.

This function is similar to subopt() but calculates secondary structures assuming the RNA sequence to be circular instead of linear

Parameters

seq
sequence
delta
fp

Returns