Functions to evaluate the free energy contributions for exterior loops. More...

Detailed Description

Functions to evaluate the free energy contributions for exterior loops.

Collaboration diagram for Exterior Loops:

Files
file	external.h
	Energy evaluation of exterior loops for MFE and partition function calculations.

Basic free energy interface
int	vrna_E_ext_stem (unsigned int type, int n5d, int n3d, vrna_param_t *p)
	Evaluate a stem branching off the exterior loop. More...

int	vrna_E_ext_loop (vrna_fold_compound_t *fc, int i, int j)
	Evaluate the free energy of a base pair in the exterior loop. More...

int	vrna_E_ext_loop_5 (vrna_fold_compound_t *fc)

int	vrna_E_ext_loop_3 (vrna_fold_compound_t *fc, int i)

Boltzmann weight (partition function) interface
typedef struct vrna_mx_pf_aux_el_s *	vrna_mx_pf_aux_el_t
	Auxiliary helper arrays for fast exterior loop computations. More...

FLT_OR_DBL	vrna_exp_E_ext_stem (unsigned int type, int n5d, int n3d, vrna_exp_param_t *p)
	Evaluate a stem branching off the exterior loop (Boltzmann factor version) More...

struct vrna_mx_pf_aux_el_s *	vrna_exp_E_ext_fast_init (vrna_fold_compound_t *fc)

void	vrna_exp_E_ext_fast_rotate (struct vrna_mx_pf_aux_el_s *aux_mx)

void	vrna_exp_E_ext_fast_free (struct vrna_mx_pf_aux_el_s *aux_mx)

FLT_OR_DBL	vrna_exp_E_ext_fast (vrna_fold_compound_t fc, int i, int j, struct vrna_mx_pf_aux_el_s aux_mx)

void	vrna_exp_E_ext_fast_update (vrna_fold_compound_t fc, int j, struct vrna_mx_pf_aux_el_s aux_mx)

Typedef Documentation

typedef struct vrna_mx_pf_aux_el_s* vrna_mx_pf_aux_el_t

#include <ViennaRNA/loops/external.h>

Auxiliary helper arrays for fast exterior loop computations.

See also: vrna_exp_E_ext_fast_init(), vrna_exp_E_ext_fast_rotate(), vrna_exp_E_ext_fast_free(), vrna_exp_E_ext_fast()

Function Documentation

int vrna_E_ext_stem	(	unsigned int	type,
		int	n5d,
		int	n3d,
		vrna_param_t *	p
	)

#include <ViennaRNA/loops/external.h>

Evaluate a stem branching off the exterior loop.

Given a base pair $(i,j)$ encoded by type, compute the energy contribution including dangling-end/terminal-mismatch contributions. Instead of returning the energy contribution per-se, this function returns the corresponding Boltzmann factor. If either of the adjacent nucleotides $(i - 1)$ and $(j+1)$ must not contribute stacking energy, the corresponding encoding must be $-1$ .

See also: vrna_E_exp_stem()

Parameters

type	The base pair encoding
n5d	The encoded nucleotide directly adjacent at the 5' side of the base pair (may be -1)
n3d	The encoded nucleotide directly adjacent at the 3' side of the base pair (may be -1)
p	The pre-computed energy parameters

Returns: The energy contribution of the introduced exterior-loop stem

int vrna_E_ext_loop	(	vrna_fold_compound_t *	fc,
		int	i,
		int	j
	)

#include <ViennaRNA/loops/external.h>

Evaluate the free energy of a base pair in the exterior loop.

Evalue the free energy of a base pair connecting two nucleotides in the exterior loop and take hard constraints into account.

Typically, this is simply dangling end contributions of the adjacent nucleotides, potentially a terminal A-U mismatch penalty, and maybe some generic soft constraint contribution for that decomposition.

Note: For dangles == 1 || 3 this function also evaluates the three additional pairs (i + 1, j), (i, j - 1), and (i + 1, j - 1) and returns the minimum for all four possibilities in total.

Parameters

fc	Fold compound to work on (defines the model and parameters)
i	5' position of the base pair
j	3' position of the base pair

Returns: Free energy contribution that arises when this pair is formed in the exterior loop

FLT_OR_DBL vrna_exp_E_ext_stem	(	unsigned int	type,
		int	n5d,
		int	n3d,
		vrna_exp_param_t *	p
	)

#include <ViennaRNA/loops/external.h>

Evaluate a stem branching off the exterior loop (Boltzmann factor version)

Given a base pair $(i,j)$ encoded by type, compute the energy contribution including dangling-end/terminal-mismatch contributions. Instead of returning the energy contribution per-se, this function returns the corresponding Boltzmann factor. If either of the adjacent nucleotides $(i - 1)$ and $(j+1)$ must not contribute stacking energy, the corresponding encoding must be $-1$ .

See also: vrna_E_ext_stem()

Parameters

type	The base pair encoding
n5d	The encoded nucleotide directly adjacent at the 5' side of the base pair (may be -1)
n3d	The encoded nucleotide directly adjacent at the 3' side of the base pair (may be -1)
p	The pre-computed energy parameters (Boltzmann factor version)

Returns: The Boltzmann weighted energy contribution of the introduced exterior-loop stem

Detailed Description

Files

Basic free energy interface

Boltzmann weight (partition function) interface

Typedef Documentation

Function Documentation