Backtracking MFE structures

Backtracking related interfaces. More...

Detailed Description

Backtracking related interfaces.

Collaboration diagram for Backtracking MFE structures:

Functions
float	vrna_backtrack5 (vrna_fold_compound_t *fc, unsigned int length, char *structure)
	Backtrack an MFE (sub)structure. More...
int	vrna_BT_hp_loop (vrna_fold_compound_t *fc, int i, int j, int en, vrna_bp_stack_t *bp_stack, int *stack_count)
	Backtrack a hairpin loop closed by . More...
int	vrna_BT_stack (vrna_fold_compound_t *fc, int *i, int *j, int *en, vrna_bp_stack_t *bp_stack, int *stack_count)
	Backtrack a stacked pair closed by .
int	vrna_BT_int_loop (vrna_fold_compound_t *fc, int *i, int *j, int en, vrna_bp_stack_t *bp_stack, int *stack_count)
	Backtrack an interior loop closed by .
int	vrna_BT_mb_loop (vrna_fold_compound_t *fc, int *i, int *j, int *k, int en, int *component1, int *component2)
	Backtrack the decomposition of a multi branch loop closed by . More...

Function Documentation

float vrna_backtrack5	(	vrna_fold_compound_t *	vc,
		unsigned int	length,
		char *	structure
	)

#include <ViennaRNA/mfe.h>

Backtrack an MFE (sub)structure.

This function allows one to backtrack the MFE structure for a (sub)sequence

Note

On error, the function returns INF / 100. and stores the empty string in structure.

Precondition

Requires pre-filled MFE dynamic programming matrices, i.e. one has to call vrna_mfe() prior to calling this function

See also

vrna_mfe(), vrna_pbacktrack5()

Parameters

fc	fold compound
length	The length of the subsequence, starting from the 5' end
structure	A pointer to the character array where the secondary structure in dot-bracket notation will be written to. (Must have size of at least $p length + 1)

Returns

The minimum free energy (MFE) for the specified length in kcal/mol and a corresponding secondary structure in dot-bracket notation (stored in structure)

SWIG Wrapper Notes:

This function is attached as overloaded method backtrack() to objects of type fold_compound with default parameter length equal to the total length of the RNA.

int vrna_BT_hp_loop	(	vrna_fold_compound_t *	fc,
		int	i,
		int	j,
		int	en,
		vrna_bp_stack_t *	bp_stack,
		int *	stack_count
	)

#include <ViennaRNA/loops/hairpin.h>

Backtrack a hairpin loop closed by .

Note

This function is polymorphic! The provided vrna_fold_compound_t may be of type VRNA_FC_TYPE_SINGLE or VRNA_FC_TYPE_COMPARATIVE

int vrna_BT_mb_loop	(	vrna_fold_compound_t *	fc,
		int *	i,
		int *	j,
		int *	k,
		int	en,
		int *	component1,
		int *	component2
	)

#include <ViennaRNA/loops/multibranch.h>

Backtrack the decomposition of a multi branch loop closed by .

Parameters

fc	The vrna_fold_compound_t filled with all relevant data for backtracking
i	5' position of base pair closing the loop (will be set to 5' position of leftmost decomposed block upon successful backtracking)
j	3' position of base pair closing the loop (will be set to 3' position of rightmost decomposed block upon successful backtracking)
k	Split position that delimits leftmost from rightmost block, [i,k] and [k+1, j], respectively. (Will be set upon successful backtracking)
en	The energy contribution of the substructure enclosed by
component1	Type of leftmost block (1 = ML, 2 = C)
component2	Type of rightmost block (1 = ML, 2 = C)

Returns

1, if backtracking succeeded, 0 otherwise.