1#ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_H__
2#define __VIENNA_RNA_PACKAGE_PART_FUNC_H__
7#define DEPRECATED(func) func __attribute__ ((deprecated))
9#define DEPRECATED(func) func
272void assign_plist_gquad_from_pr(
plist **pl,
276char *get_centroid_struct_gquad_pr(
int length,
386 unsigned int length);
388plist *stackProb(
double cutoff);
413DEPRECATED(
char *
centroid(
int length,
442 const char *
string));
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
double * pr
A pointer to the base pair probability matrix.
char * get_centroid_struct_pl(int length, double *dist, plist *pl)
Get the centroid structure of the ensemble.
char * get_centroid_struct_pr(int length, double *dist, double *pr)
Get the centroid structure of the ensemble.
void assign_plist_from_pr(plist **pl, double *probs, int length, double cutoff)
Create a plist from a probability matrix.
void update_pf_params_par(int length, pf_paramT *parameters)
Recalculate energy parameters.
float pf_fold_par(const char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular)
Compute the partition function for a given RNA sequence.
int get_pf_arrays(short **S_p, short **S1_p, char **ptype_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p)
Get the pointers to (almost) all relavant computation arrays used in partition function computation.
void update_pf_params(int length)
Recalculate energy parameters.
double mean_bp_distance_pr(int length, double *pr)
Get the mean base pair distance in the thermodynamic ensemble.
double mean_bp_distance(int length)
Get the mean base pair distance of the last partition function computation.
float pf_circ_fold(const char *sequence, char *structure)
Compute the partition function of a circular RNA sequence.
double * export_bppm(void)
Get a pointer to the base pair probability array.
float pf_fold(const char *sequence, char *structure)
Compute the partition function of an RNA sequence.
void free_pf_arrays(void)
Free arrays for the partition function recursions.
char * pbacktrack_circ(char *sequence)
Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability.
char * pbacktrack(char *sequence)
Sample a secondary structure from the Boltzmann ensemble according its probability .
int st_back
Flag indicating that auxilary arrays are needed throughout the computations. This is essential for st...
void init_pf_fold(int length)
Allocate space for pf_fold()
double get_subseq_F(int i, int j)
Get the free energy of a subsequence from the q[] array.
void bppm_to_structure(char *structure, double *pr, unsigned int length)
Create a dot-bracket like structure string from base pair probability matrix.
char bppm_symbol(const float *x)
Get a pseudo dot bracket notation for a given probability information.
double expLoopEnergy(int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)
double expHairpinEnergy(int u, int type, short si1, short sj1, const char *string)
char * centroid(int length, double *dist)
double mean_bp_dist(int length)
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition data_structures.h:203
this datastructure is used as input parameter in functions of PS_dot.h and others
Definition data_structures.h:48