RNAlib-2.2.9
part_func.h
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1 #ifndef VIENNA_RNA_PACKAGE_PART_FUNC_H
2 #define VIENNA_RNA_PACKAGE_PART_FUNC_H
3 
4 /* make this interface backward compatible with RNAlib < 2.2.0 */
5 #define VRNA_BACKWARD_COMPAT
6 
8 #include <ViennaRNA/params.h>
9 #include <ViennaRNA/centroid.h>
12 
13 #ifdef DEPRECATION_WARNINGS
14 # ifdef __GNUC__
15 # define DEPRECATED(func) func __attribute__ ((deprecated))
16 # else
17 # define DEPRECATED(func) func
18 # endif
19 #else
20 # define DEPRECATED(func) func
21 #endif
22 
41 /*
42 #################################################
43 # PARTITION FUNCTION COMPUTATION #
44 #################################################
45 */
46 
73 float vrna_pf(vrna_fold_compound_t *vc, char *structure);
74 
98 float vrna_pf_fold(const char *sequence, char *structure, vrna_plist_t **pl);
99 
126 float vrna_pf_circfold(const char *sequence, char *structure, vrna_plist_t **pl);
127 
128 /*
129 #################################################
130 # OTHER PARTITION FUNCTION RELATED DECLARATIONS #
131 #################################################
132 */
133 
141 int vrna_pf_float_precision(void);
142 
143 #ifdef VRNA_BACKWARD_COMPAT
144 
145 /*
146 #################################################
147 # DEPRECATED FUNCTIONS #
148 #################################################
149 */
150 
163 extern int st_back;
164 
205 DEPRECATED(float pf_fold_par( const char *sequence,
206  char *structure,
207  vrna_exp_param_t *parameters,
208  int calculate_bppm,
209  int is_constrained,
210  int is_circular));
211 
251 DEPRECATED(float pf_fold(const char *sequence,
252  char *structure));
253 
280 DEPRECATED(float pf_circ_fold( const char *sequence,
281  char *structure));
282 
293 DEPRECATED(char *pbacktrack(char *sequence));
294 
295 DEPRECATED(char *pbacktrack5(char *sequence, int length));
296 
312 DEPRECATED(char *pbacktrack_circ(char *sequence));
313 
332 DEPRECATED(void free_pf_arrays(void));
333 
344 DEPRECATED(void update_pf_params(int length));
345 
353 DEPRECATED(void update_pf_params_par(int length, vrna_exp_param_t *parameters));
354 
371 DEPRECATED(FLT_OR_DBL *export_bppm(void));
372 
373 
389 DEPRECATED(int get_pf_arrays(short **S_p,
390  short **S1_p,
391  char **ptype_p,
392  FLT_OR_DBL **qb_p,
393  FLT_OR_DBL **qm_p,
394  FLT_OR_DBL **q1k_p,
395  FLT_OR_DBL **qln_p));
396 
400 DEPRECATED(double get_subseq_F(int i, int j));
401 
402 
414 DEPRECATED(double mean_bp_distance(int length));
415 
433 DEPRECATED(double mean_bp_distance_pr(int length, FLT_OR_DBL *pr));
434 
440 DEPRECATED(vrna_plist_t *stackProb(double cutoff));
441 
442 
448 DEPRECATED(void init_pf_fold(int length));
449 
454 DEPRECATED(char *centroid(int length, double *dist));
455 
460 DEPRECATED(char *get_centroid_struct_gquad_pr(int length,
461  double *dist));
462 
468 DEPRECATED(double mean_bp_dist(int length));
469 
473 DEPRECATED(double expLoopEnergy(int u1,
474  int u2,
475  int type,
476  int type2,
477  short si1,
478  short sj1,
479  short sp1,
480  short sq1));
481 
485 DEPRECATED(double expHairpinEnergy( int u,
486  int type,
487  short si1,
488  short sj1,
489  const char *string));
490 
491 /* this doesn't work if free_pf_arrays() is called before */
492 DEPRECATED(void assign_plist_gquad_from_pr(vrna_plist_t **pl,
493  int length,
494  double cut_off));
495 
496 #endif
497 
498 #endif
float pf_circ_fold(const char *sequence, char *structure)
Compute the partition function of a circular RNA sequence.
char * get_centroid_struct_gquad_pr(int length, double *dist)
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:424
Equilibrium Probability implementations.
double expHairpinEnergy(int u, int type, short si1, short sj1, const char *string)
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.
float vrna_pf_circfold(const char *sequence, char *structure, vrna_plist_t **pl)
Compute Partition function (and base pair probabilities) for a circular RNA sequences using a compar...
double mean_bp_distance(int length)
Get the mean base pair distance of the last partition function computation.
float vrna_pf_fold(const char *sequence, char *structure, vrna_plist_t **pl)
Compute Partition function (and base pair probabilities) for an RNA sequence using a comparative met...
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:164
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.