RNAlib-2.2.0-RC2
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MFE calculations for single RNA sequences. More...
Go to the source code of this file.
Functions | |
float | vrna_fold (vrna_fold_compound *vc, char *structure) |
Compute minimum free energy and an appropriate secondary structure of an 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) |
MFE calculations for single RNA sequences.
This file includes (almost) all function declarations within the RNAlib that are related to MFE folding...
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 | ) |
Allocate arrays for folding
{This function is deprecated and will be removed soon!}
See vrna_fold() and vrna_fold_compound for the usage of the new API!