RNAlib-2.2.0-RC2
part_func.h
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1 #ifndef VIENNA_RNA_PACKAGE_PART_FUNC_H
2 #define VIENNA_RNA_PACKAGE_PART_FUNC_H
3 
5 #include <ViennaRNA/params.h>
6 #include <ViennaRNA/centroid.h>
7 
8 #ifdef __GNUC__
9 #define DEPRECATED(func) func __attribute__ ((deprecated))
10 #else
11 #define DEPRECATED(func) func
12 #endif
13 
14 
15 
44 extern int st_back;
45 
46 /*
47 #################################################
48 # PARTITION FUNCTION COMPUTATION #
49 #################################################
50 */
51 
82  char *structure);
83 
124 DEPRECATED(float pf_fold_par( const char *sequence,
125  char *structure,
126  vrna_exp_param_t *parameters,
127  int calculate_bppm,
128  int is_constrained,
129  int is_circular));
130 
170 DEPRECATED(float pf_fold(const char *sequence,
171  char *structure));
172 
199 DEPRECATED(float pf_circ_fold( const char *sequence,
200  char *structure));
201 
212 DEPRECATED(char *pbacktrack(char *sequence));
213 
214 DEPRECATED(char *pbacktrack5(char *sequence, int length));
215 
227 char *vrna_pbacktrack5(vrna_fold_compound *vc, int length);
228 
244 
260 DEPRECATED(char *pbacktrack_circ(char *sequence));
261 
280 DEPRECATED(void free_pf_arrays(void));
281 
292 DEPRECATED(void update_pf_params(int length));
293 
301 DEPRECATED(void update_pf_params_par(int length, vrna_exp_param_t *parameters));
302 
303 
319  vrna_exp_param_t *params);
320 
360  double *mfe);
361 
378 DEPRECATED(FLT_OR_DBL *export_bppm(void));
379 
380 /*
381 #################################################
382 # OTHER PARTITION FUNCTION RELATED DECLARATIONS #
383 #################################################
384 */
385 
386 
402 int get_pf_arrays(short **S_p,
403  short **S1_p,
404  char **ptype_p,
405  FLT_OR_DBL **qb_p,
406  FLT_OR_DBL **qm_p,
407  FLT_OR_DBL **q1k_p,
408  FLT_OR_DBL **qln_p);
409 
413 double get_subseq_F(int i, int j);
414 
415 
427 DEPRECATED(double mean_bp_distance(int length));
428 
446 DEPRECATED(double mean_bp_distance_pr(int length, FLT_OR_DBL *pr));
447 
461 double vrna_mean_bp_distance_pr(int length, FLT_OR_DBL *pr);
462 
476 
477 plist *stackProb(double cutoff);
478 
479 
480 /*
481 #################################################
482 # DEPRECATED FUNCTIONS #
483 #################################################
484 */
485 
491 DEPRECATED(void init_pf_fold(int length));
492 
497 DEPRECATED(char *centroid(int length, double *dist));
498 
503 DEPRECATED(char *get_centroid_struct_gquad_pr(int length,
504  double *dist));
505 
511 DEPRECATED(double mean_bp_dist(int length));
512 
516 DEPRECATED(double expLoopEnergy(int u1,
517  int u2,
518  int type,
519  int type2,
520  short si1,
521  short sj1,
522  short sp1,
523  short sq1));
524 
528 DEPRECATED(double expHairpinEnergy( int u,
529  int type,
530  short si1,
531  short sj1,
532  const char *string));
533 
534 /* this doesn't work if free_pf_arrays() is called before */
535 DEPRECATED(void assign_plist_gquad_from_pr(plist **pl,
536  int length,
537  double cut_off));
538 
539 #endif
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.