1 #ifndef VIENNA_RNA_PACKAGE_PART_FUNC_H
2 #define VIENNA_RNA_PACKAGE_PART_FUNC_H
5 #define VRNA_BACKWARD_COMPAT
12 #ifdef DEPRECATION_WARNINGS
14 # define DEPRECATED(func) func __attribute__ ((deprecated))
16 # define DEPRECATED(func) func
19 # define DEPRECATED(func) func
185 #ifdef VRNA_BACKWARD_COMPAT
247 DEPRECATED(
float pf_fold_par(
const char *sequence,
293 DEPRECATED(
float pf_fold(
const char *sequence,
337 DEPRECATED(
char *pbacktrack5(
char *sequence,
int length));
496 DEPRECATED(
char *
centroid(
int length,
double *dist));
531 const char *
string));
534 DEPRECATED(
void assign_plist_gquad_from_pr(
vrna_plist_t **pl,
float pf_circ_fold(const char *sequence, char *structure)
Compute the partition function of a circular RNA sequence.
float vrna_pf_fold(const char *seq, char *structure, vrna_plist_t **pl)
Compute Partition function (and base pair probabilities) for an RNA sequence using a comparative met...
char * get_centroid_struct_gquad_pr(int length, double *dist)
float vrna_pf_circfold(const char *seq, char *structure, vrna_plist_t **pl)
Compute Partition function (and base pair probabilities) for a circular RNA sequences using a compar...
double vrna_mean_bp_distance(vrna_fold_compound_t *vc)
Get the mean base pair distance in the thermodynamic ensemble.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:39
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:390
double expHairpinEnergy(int u, int type, short si1, short sj1, const char *string)
vrna_plist_t * vrna_stack_prob(vrna_fold_compound_t *vc, double cutoff)
Compute stacking probabilities.
double get_subseq_F(int i, int j)
Get the free energy of a subsequence from the q[] array.
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 vrna_pf(vrna_fold_compound_t *vc, char *structure)
Compute the partition function for a given RNA sequence, or sequence alignment.
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...
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
Boltzmann Sampling of secondary structures from the ensemble.
void free_pf_arrays(void)
Free arrays for the partition function recursions.
double mean_bp_distance(int length)
Get the mean base pair distance of the last partition function computation.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:164
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.
vrna_plist_t * stackProb(double cutoff)
Get the probability of stacks.
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)
int vrna_pf_float_precision(void)
Find out whether partition function computations are using single precision floating points...
double mean_bp_dist(int length)
Centroid structure computation.