RNAlib-2.2.7
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This module contains all functions and variables related to the calculation of global minimum free energy structures for single sequences. More...
Functions | |
float | vrna_fold (const char *string, char *structure) |
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence. More... | |
float | vrna_circfold (const char *string, char *structure) |
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for a circular RNA sequence. More... | |
float | fold_par (const char *sequence, char *structure, vrna_param_t *parameters, int is_constrained, int is_circular) |
Compute minimum free energy and an appropriate secondary structure of an RNA sequence. More... | |
float | fold (const char *sequence, char *structure) |
Compute minimum free energy and an appropriate secondary structure of an RNA sequence. More... | |
float | circfold (const char *sequence, char *structure) |
Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence. More... | |
void | free_arrays (void) |
Free arrays for mfe folding. More... | |
void | update_fold_params (void) |
Recalculate energy parameters. More... | |
void | update_fold_params_par (vrna_param_t *parameters) |
Recalculate energy parameters. More... | |
void | export_fold_arrays (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p) |
void | export_fold_arrays_par (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p, vrna_param_t **P_p) |
void | export_circfold_arrays (int *Fc_p, int *FcH_p, int *FcI_p, int *FcM_p, int **fM2_p, int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p) |
void | export_circfold_arrays_par (int *Fc_p, int *FcH_p, int *FcI_p, int *FcM_p, int **fM2_p, int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p, vrna_param_t **P_p) |
int | LoopEnergy (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1) |
int | HairpinE (int size, int type, int si1, int sj1, const char *string) |
void | initialize_fold (int length) |
This module contains all functions and variables related to the calculation of global minimum free energy structures for single sequences.
The library provides a fast dynamic programming minimum free energy folding algorithm as described by "Zuker & Stiegler (1981)" [19].
float vrna_fold | ( | const char * | string, |
char * | structure | ||
) |
#include <ViennaRNA/fold.h>
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence.
This simplified interface to vrna_mfe() computes the MFE and, if required, a secondary structure for an RNA sequence using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing, e.g. suboptimal backtracking, etc.
sequence | RNA sequence |
structure | A pointer to the character array where the secondary structure in dot-bracket notation will be written to |
float vrna_circfold | ( | const char * | string, |
char * | structure | ||
) |
#include <ViennaRNA/fold.h>
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for a circular RNA sequence.
This simplified interface to vrna_mfe() computes the MFE and, if required, a secondary structure for a circular RNA sequence using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing, e.g. suboptimal backtracking, etc.
Folding of circular RNA sequences is handled as a post-processing step of the forward recursions. See [6] for further details.
sequence | RNA sequence |
structure | A pointer to the character array where the secondary structure in dot-bracket notation will be written to |
float fold_par | ( | const char * | sequence, |
char * | structure, | ||
vrna_param_t * | parameters, | ||
int | is_constrained, | ||
int | is_circular | ||
) |
#include <ViennaRNA/fold.h>
Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
The first parameter given, the RNA sequence, must be uppercase and should only contain an alphabet that is understood by the RNAlib
(e.g. )
The second parameter, structure, must always point to an allocated block of memory with a size of at least
If the third parameter is NULL, global model detail settings are assumed for the folding recursions. Otherwise, the provided parameters are used.
The fourth parameter indicates whether a secondary structure constraint in enhanced dot-bracket notation is passed through the structure parameter or not. If so, the characters " | x < > " are recognized to mark bases that are paired, unpaired, paired upstream, or downstream, respectively. Matching brackets " ( ) " denote base pairs, dots "." are used for unconstrained bases.
To indicate that the RNA sequence is circular and thus has to be post-processed, set the last parameter to non-zero
After a successful call of fold_par(), a backtracked secondary structure (in dot-bracket notation) that exhibits the minimum of free energy will be written to the memory structure is pointing to. The function returns the minimum of free energy for any fold of the sequence given.
sequence | RNA sequence |
structure | A pointer to the character array where the secondary structure in dot-bracket notation will be written to |
parameters | A data structure containing the prescaled energy contributions and the model details. (NULL may be passed, see OpenMP notes above) |
is_constrained | Switch to indicate that a structure contraint is passed via the structure argument (0==off) |
is_circular | Switch to (de-)activate postprocessing steps in case RNA sequence is circular (0==off) |
float fold | ( | const char * | sequence, |
char * | structure | ||
) |
#include <ViennaRNA/fold.h>
Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
This function essentially does the same thing as fold_par(). However, it takes its model details, i.e. temperature, dangles, tetra_loop, noGU, no_closingGU, fold_constrained, noLonelyPairs from the current global settings within the library
sequence | RNA sequence |
structure | A pointer to the character array where the secondary structure in dot-bracket notation will be written to |
float circfold | ( | const char * | sequence, |
char * | structure | ||
) |
#include <ViennaRNA/fold.h>
Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence.
This function essentially does the same thing as fold_par(). However, it takes its model details, i.e. temperature, dangles, tetra_loop, noGU, no_closingGU, fold_constrained, noLonelyPairs from the current global settings within the library
sequence | RNA sequence |
structure | A pointer to the character array where the secondary structure in dot-bracket notation will be written to |
void free_arrays | ( | void | ) |
#include <ViennaRNA/fold.h>
Free arrays for mfe folding.
void update_fold_params | ( | void | ) |
#include <ViennaRNA/fold.h>
Recalculate energy parameters.
void update_fold_params_par | ( | vrna_param_t * | parameters | ) |
#include <ViennaRNA/fold.h>
Recalculate energy parameters.
void export_fold_arrays | ( | int ** | f5_p, |
int ** | c_p, | ||
int ** | fML_p, | ||
int ** | fM1_p, | ||
int ** | indx_p, | ||
char ** | ptype_p | ||
) |
#include <ViennaRNA/fold.h>
void export_fold_arrays_par | ( | int ** | f5_p, |
int ** | c_p, | ||
int ** | fML_p, | ||
int ** | fM1_p, | ||
int ** | indx_p, | ||
char ** | ptype_p, | ||
vrna_param_t ** | P_p | ||
) |
#include <ViennaRNA/fold.h>
void export_circfold_arrays | ( | int * | Fc_p, |
int * | FcH_p, | ||
int * | FcI_p, | ||
int * | FcM_p, | ||
int ** | fM2_p, | ||
int ** | f5_p, | ||
int ** | c_p, | ||
int ** | fML_p, | ||
int ** | fM1_p, | ||
int ** | indx_p, | ||
char ** | ptype_p | ||
) |
#include <ViennaRNA/fold.h>
void export_circfold_arrays_par | ( | int * | Fc_p, |
int * | FcH_p, | ||
int * | FcI_p, | ||
int * | FcM_p, | ||
int ** | fM2_p, | ||
int ** | f5_p, | ||
int ** | c_p, | ||
int ** | fML_p, | ||
int ** | fM1_p, | ||
int ** | indx_p, | ||
char ** | ptype_p, | ||
vrna_param_t ** | P_p | ||
) |
#include <ViennaRNA/fold.h>
int LoopEnergy | ( | int | n1, |
int | n2, | ||
int | type, | ||
int | type_2, | ||
int | si1, | ||
int | sj1, | ||
int | sp1, | ||
int | sq1 | ||
) |
#include <ViennaRNA/fold.h>
int HairpinE | ( | int | size, |
int | type, | ||
int | si1, | ||
int | sj1, | ||
const char * | string | ||
) |
#include <ViennaRNA/fold.h>
void initialize_fold | ( | int | length | ) |
#include <ViennaRNA/fold.h>
Allocate arrays for folding