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RNAlib-2.4.17
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Functions to evaluate the free energy contributions for exterior loops. More...
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 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
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
and
must not contribute stacking energy, the corresponding encoding must be
.
| 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_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.
| 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
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
and
must not contribute stacking energy, the corresponding encoding must be
.
| 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) |