RNAlib-2.5.1

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.
 

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...
 
vrna_mx_pf_aux_el_t vrna_exp_E_ext_fast_init (vrna_fold_compound_t *fc)
 
void vrna_exp_E_ext_fast_rotate (vrna_mx_pf_aux_el_t aux_mx)
 
void vrna_exp_E_ext_fast_free (vrna_mx_pf_aux_el_t aux_mx)
 
FLT_OR_DBL vrna_exp_E_ext_fast (vrna_fold_compound_t *fc, int i, int j, vrna_mx_pf_aux_el_t aux_mx)
 
void vrna_exp_E_ext_fast_update (vrna_fold_compound_t *fc, int j, vrna_mx_pf_aux_el_t aux_mx)
 

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_eval_ext_stem (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)
 

Typedef Documentation

◆ vrna_mx_pf_aux_el_t

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

◆ vrna_E_ext_stem()

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
typeThe base pair encoding
n5dThe encoded nucleotide directly adjacent at the 5' side of the base pair (may be -1)
n3dThe encoded nucleotide directly adjacent at the 3' side of the base pair (may be -1)
pThe pre-computed energy parameters
Returns
The energy contribution of the introduced exterior-loop stem

◆ vrna_eval_ext_stem()

int vrna_eval_ext_stem ( 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
fcFold compound to work on (defines the model and parameters)
i5' position of the base pair
j3' position of the base pair
Returns
Free energy contribution that arises when this pair is formed in the exterior loop

◆ vrna_exp_E_ext_stem()

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
typeThe base pair encoding
n5dThe encoded nucleotide directly adjacent at the 5' side of the base pair (may be -1)
n3dThe encoded nucleotide directly adjacent at the 3' side of the base pair (may be -1)
pThe pre-computed energy parameters (Boltzmann factor version)
Returns
The Boltzmann weighted energy contribution of the introduced exterior-loop stem