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