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RNAlib-2.4.17
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Functions to evaluate the free energy contributions for hairpin loops. More...
Functions to evaluate the free energy contributions for hairpin loops.
Collaboration diagram for Hairpin Loops:Files | |
| file | hairpin.h |
| Energy evaluation of hairpin loops for MFE and partition function calculations. | |
Basic free energy interface | |
| int | vrna_E_hp_loop (vrna_fold_compound_t *fc, int i, int j) |
| Evaluate the free energy of a hairpin loop and consider hard constraints if they apply. More... | |
| int | vrna_E_ext_hp_loop (vrna_fold_compound_t *fc, int i, int j) |
| Evaluate the free energy of an exterior hairpin loop and consider possible hard constraints. More... | |
| int | vrna_eval_ext_hp_loop (vrna_fold_compound_t *fc, int i, int j) |
| Evaluate free energy of an exterior hairpin loop. | |
| int | vrna_eval_hp_loop (vrna_fold_compound_t *fc, int i, int j) |
| Evaluate free energy of a hairpin loop. More... | |
| PRIVATE int | E_Hairpin (int size, int type, int si1, int sj1, const char *string, vrna_param_t *P) |
| Compute the Energy of a hairpin-loop. More... | |
Boltzmann weight (partition function) interface | |
| PRIVATE FLT_OR_DBL | exp_E_Hairpin (int u, int type, short si1, short sj1, const char *string, vrna_exp_param_t *P) |
| Compute Boltzmann weight | |
| FLT_OR_DBL | vrna_exp_E_hp_loop (vrna_fold_compound_t *fc, int i, int j) |
| High-Level function for hairpin loop energy evaluation (partition function variant) More... | |
| int vrna_E_hp_loop | ( | vrna_fold_compound_t * | fc, |
| int | i, | ||
| int | j | ||
| ) |
#include <ViennaRNA/loops/hairpin.h>
Evaluate the free energy of a hairpin loop and consider hard constraints if they apply.
This function evaluates the free energy of a hairpin loop
In case the base pair is not allowed due to a constraint conflict, this function returns INF.
| fc | The vrna_fold_compound_t that stores all relevant model settings |
| i | The 5' nucleotide of the base pair (3' to evaluate the pair as exterior hairpin loop) |
| j | The 3' nucleotide of the base pair (5' to evaluate the pair as exterior hairpin loop) |
| int vrna_E_ext_hp_loop | ( | vrna_fold_compound_t * | fc, |
| int | i, | ||
| int | j | ||
| ) |
#include <ViennaRNA/loops/hairpin.h>
Evaluate the free energy of an exterior hairpin loop and consider possible hard constraints.
| int vrna_eval_hp_loop | ( | vrna_fold_compound_t * | fc, |
| int | i, | ||
| int | j | ||
| ) |
#include <ViennaRNA/loops/hairpin.h>
Evaluate free energy of a hairpin loop.
| fc | The vrna_fold_compound_t for the particular energy evaluation |
| i | 5'-position of the base pair |
| j | 3'-position of the base pair |
| PRIVATE int E_Hairpin | ( | int | size, |
| int | type, | ||
| int | si1, | ||
| int | sj1, | ||
| const char * | string, | ||
| vrna_param_t * | P | ||
| ) |
#include <ViennaRNA/loops/hairpin.h>
Compute the Energy of a hairpin-loop.
To evaluate the free energy of a hairpin-loop, several parameters have to be known. A general hairpin-loop has this structure:
a3 a4
a2 a5
a1 a6
X - Y
| |
5' 3'
where X-Y marks the closing pair [e.g. a (G,C) pair]. The length of this loop is 6 as there are six unpaired nucleotides (a1-a6) enclosed by (X,Y). The 5' mismatching nucleotide is a1 while the 3' mismatch is a6. The nucleotide sequence of this loop is "a1.a2.a3.a4.a5.a6"
| size | The size of the loop (number of unpaired nucleotides) |
| type | The pair type of the base pair closing the hairpin |
| si1 | The 5'-mismatching nucleotide |
| sj1 | The 3'-mismatching nucleotide |
| string | The sequence of the loop (May be NULL, otherwise mst be at least |
| P | The datastructure containing scaled energy parameters |
| PRIVATE FLT_OR_DBL exp_E_Hairpin | ( | int | u, |
| int | type, | ||
| short | si1, | ||
| short | sj1, | ||
| const char * | string, | ||
| vrna_exp_param_t * | P | ||
| ) |
#include <ViennaRNA/loops/hairpin.h>
Compute Boltzmann weight
of a hairpin loop.
multiply by scale[u+2]
| u | The size of the loop (number of unpaired nucleotides) |
| type | The pair type of the base pair closing the hairpin |
| si1 | The 5'-mismatching nucleotide |
| sj1 | The 3'-mismatching nucleotide |
| string | The sequence of the loop (May be NULL, otherwise mst be at least |
| P | The datastructure containing scaled Boltzmann weights of the energy parameters |
| FLT_OR_DBL vrna_exp_E_hp_loop | ( | vrna_fold_compound_t * | fc, |
| int | i, | ||
| int | j | ||
| ) |
#include <ViennaRNA/loops/hairpin.h>
High-Level function for hairpin loop energy evaluation (partition function variant)