RNAlib-2.2.0RC0
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/centroid.h>
6 
7 #ifdef __GNUC__
8 #define DEPRECATED(func) func __attribute__ ((deprecated))
9 #else
10 #define DEPRECATED(func) func
11 #endif
12 
13 
14 
43 extern int st_back;
44 
45 /*
46 #################################################
47 # PARTITION FUNCTION COMPUTATION #
48 #################################################
49 */
50 
81  char *structure);
82 
123 DEPRECATED(float pf_fold_par( const char *sequence,
124  char *structure,
125  pf_paramT *parameters,
126  int calculate_bppm,
127  int is_constrained,
128  int is_circular));
129 
169 DEPRECATED(float pf_fold(const char *sequence,
170  char *structure));
171 
198 DEPRECATED(float pf_circ_fold( const char *sequence,
199  char *structure));
200 
211 DEPRECATED(char *pbacktrack(char *sequence));
212 
213 DEPRECATED(char *pbacktrack5(char *sequence, int length));
214 
226 char *vrna_pbacktrack5(vrna_fold_compound *vc, int length);
227 
243 
259 DEPRECATED(char *pbacktrack_circ(char *sequence));
260 
279 DEPRECATED(void free_pf_arrays(void));
280 
291 DEPRECATED(void update_pf_params(int length));
292 
300 DEPRECATED(void update_pf_params_par(int length, pf_paramT *parameters));
301 
302 
318  pf_paramT *params);
319 
359  double *mfe);
360 
377 DEPRECATED(FLT_OR_DBL *export_bppm(void));
378 
379 /*
380 #################################################
381 # OTHER PARTITION FUNCTION RELATED DECLARATIONS #
382 #################################################
383 */
384 
385 
401 int get_pf_arrays(short **S_p,
402  short **S1_p,
403  char **ptype_p,
404  FLT_OR_DBL **qb_p,
405  FLT_OR_DBL **qm_p,
406  FLT_OR_DBL **q1k_p,
407  FLT_OR_DBL **qln_p);
408 
412 double get_subseq_F(int i, int j);
413 
414 
426 DEPRECATED(double mean_bp_distance(int length));
427 
445 DEPRECATED(double mean_bp_distance_pr(int length, FLT_OR_DBL *pr));
446 
460 double vrna_mean_bp_distance_pr(int length, FLT_OR_DBL *pr);
461 
475 
476 plist *stackProb(double cutoff);
477 
478 
479 /*
480 #################################################
481 # DEPRECATED FUNCTIONS #
482 #################################################
483 */
484 
490 DEPRECATED(void init_pf_fold(int length));
491 
496 DEPRECATED(char *centroid(int length, double *dist));
497 
502 DEPRECATED(char *get_centroid_struct_gquad_pr(int length,
503  double *dist));
504 
510 DEPRECATED(double mean_bp_dist(int length));
511 
515 DEPRECATED(double expLoopEnergy(int u1,
516  int u2,
517  int type,
518  int type2,
519  short si1,
520  short sj1,
521  short sp1,
522  short sq1));
523 
527 DEPRECATED(double expHairpinEnergy( int u,
528  int type,
529  short si1,
530  short sj1,
531  const char *string));
532 
533 /* this doesn't work if free_pf_arrays() is called before */
534 DEPRECATED(void assign_plist_gquad_from_pr(plist **pl,
535  int length,
536  double cut_off));
537 
538 #endif
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.
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)
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: data_structures.h:225
double get_subseq_F(int i, int j)
Get the free energy of a subsequence from the q[] array.
Definition: data_structures.h:359
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
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:94
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...
void vrna_update_pf_params(vrna_fold_compound *vc, pf_paramT *params)
Update the energy parameters for subsequent partition function computations.
char * pbacktrack(char *sequence)
Sample a secondary structure from the Boltzmann ensemble according its probability ...
double expLoopEnergy(int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)
double mean_bp_dist(int length)
void vrna_rescale_pf_params(vrna_fold_compound *vc, double *mfe)
Rescale Boltzmann factors for partition function computations.
void update_pf_params_par(int length, pf_paramT *parameters)
Recalculate energy parameters.
Centroid structure computation.