1 #ifndef VIENNA_RNA_PACKAGE_FOLD_H 2 #define VIENNA_RNA_PACKAGE_FOLD_H 9 #ifdef VRNA_WARN_DEPRECATED 10 # if defined(__clang__) 11 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg))) 12 # elif defined(__GNUC__) 13 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg))) 15 # define DEPRECATED(func, msg) func 18 # define DEPRECATED(func, msg) func 85 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 136 "Use the new API and vrna_mfe() instead");
154 DEPRECATED(
float fold(
const char *sequence,
char *structure),
155 "Use vrna_fold() or vrna_mfe() instead");
173 DEPRECATED(
float circfold(
const char *sequence,
char *structure),
174 "Use vrna_circfold() or vrna_mfe() instead");
184 "This function is obsolete");
195 "This function is obsolete");
204 "Use the new API with vrna_fold_compound_t datastructure instead");
218 "Use the new API with vrna_fold_compound_t datastructure instead");
233 "Use the new API with vrna_fold_compound_t datastructure instead");
252 "Use the new API with vrna_fold_compound_t datastructure instead");
272 "Use the new API with vrna_fold_compound_t datastructure instead");
294 "This function is obsolete");
305 "Use E_Hairpin() instead");
313 "This function is obsolete");
318 DEPRECATED(
char *backtrack_fold_from_pair(
char *sequence,
321 "This function is obsolete. Consider using vrna_backtrack_from_intervals() instead");
void free_arrays(void)
Free arrays for mfe folding.
int HairpinE(int size, int type, int si1, int sj1, const char *string)
void update_fold_params_par(vrna_param_t *parameters)
Recalculate energy parameters.
void initialize_fold(int length)
float vrna_circfold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for a circular RNA sequenc...
float circfold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence...
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:56
Various data structures and pre-processor macros.
Functions to deal with sets of energy parameters.
float vrna_fold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence...
void export_fold_arrays(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p)
float fold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
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 update_fold_params(void)
Recalculate energy parameters.
int LoopEnergy(int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)
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.
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
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)
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)
Functions and variables related to energy evaluation of sequence/structure pairs. ...