1 #ifndef VIENNA_RNA_PACKAGE_PART_FUNC_H
2 #define VIENNA_RNA_PACKAGE_PART_FUNC_H
9 #define DEPRECATED(func) func __attribute__ ((deprecated))
11 #define DEPRECATED(func) func
124 DEPRECATED(
float pf_fold_par(
const char *sequence,
170 DEPRECATED(
float pf_fold(
const char *sequence,
214 DEPRECATED(
char *pbacktrack5(
char *sequence,
int length));
477 plist *stackProb(
double cutoff);
497 DEPRECATED(
char *
centroid(
int length,
double *dist));
532 const char *
string));
535 DEPRECATED(
void assign_plist_gquad_from_pr(
plist **pl,
char * vrna_pbacktrack(vrna_fold_compound *vc)
Sample a secondary structure from the Boltzmann ensemble according its probability ...
float pf_circ_fold(const char *sequence, char *structure)
Compute the partition function of a circular RNA sequence.
double vrna_mean_bp_distance(vrna_fold_compound *vc)
Get the mean base pair distance in the thermodynamic ensemble.
char * get_centroid_struct_gquad_pr(int length, double *dist)
char * vrna_pbacktrack5(vrna_fold_compound *vc, int length)
Sample a secondary structure of a subsequence from the Boltzmann ensemble according its probability ...
double expHairpinEnergy(int u, int type, short si1, short sj1, const char *string)
void vrna_update_pf_params(vrna_fold_compound *vc, vrna_exp_param_t *params)
Update the energy parameters for subsequent partition function computations.
double get_subseq_F(int i, int j)
Get the free energy of a subsequence from the q[] array.
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:689
void update_pf_params_par(int length, vrna_exp_param_t *parameters)
Recalculate energy parameters.
void init_pf_fold(int length)
Allocate space for pf_fold()
int st_back
Flag indicating that auxilary arrays are needed throughout the computations. This is essential for st...
char * centroid(int length, double *dist)
float pf_fold(const char *sequence, char *structure)
Compute the partition function of an RNA sequence.
FLT_OR_DBL * export_bppm(void)
Get a pointer to the base pair probability arrayAccessing the base pair probabilities for a pair (i...
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:45
void free_pf_arrays(void)
Free arrays for the partition function recursions.
float vrna_pf_fold(vrna_fold_compound *vc, char *structure)
Compute the partition function for a given RNA sequence.
double mean_bp_distance(int length)
Get the mean base pair distance of the last partition function computation.
double vrna_mean_bp_distance_pr(int length, FLT_OR_DBL *pr)
Get the mean base pair distance in the thermodynamic ensemble from a probability matrix.
char * pbacktrack_circ(char *sequence)
Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability...
void update_pf_params(int length)
Recalculate energy parameters.
double mean_bp_distance_pr(int length, FLT_OR_DBL *pr)
Get the mean base pair distance in the thermodynamic ensemble.
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
int get_pf_arrays(short **S_p, short **S1_p, char **ptype_p, FLT_OR_DBL **qb_p, FLT_OR_DBL **qm_p, FLT_OR_DBL **q1k_p, FLT_OR_DBL **qln_p)
Get the pointers to (almost) all relavant computation arrays used in partition function computation...
char * pbacktrack(char *sequence)
Sample a secondary structure from the Boltzmann ensemble according its probability ...
float pf_fold_par(const char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained, int is_circular)
Compute the partition function for a given RNA sequence.
double expLoopEnergy(int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:86
double mean_bp_dist(int length)
void vrna_rescale_pf_params(vrna_fold_compound *vc, double *mfe)
Rescale Boltzmann factors for partition function computations.
Centroid structure computation.