RNAlib-2.2.9

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part_func.h
Go to the documentation of this file.
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
7 #include <ViennaRNA/data_structures.h>
8 #include <ViennaRNA/params.h>
9 #include <ViennaRNA/centroid.h>
10 #include <ViennaRNA/equilibrium_probs.h>
11 #include <ViennaRNA/boltzmann_sampling.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
pf_circ_fold
float pf_circ_fold(const char *sequence, char *structure)
Compute the partition function of a circular RNA sequence.
get_centroid_struct_gquad_pr
char * get_centroid_struct_gquad_pr(int length, double *dist)
FLT_OR_DBL
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:39
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:424
equilibrium_probs.h
Equilibrium Probability implementations.
expHairpinEnergy
double expHairpinEnergy(int u, int type, short si1, short sj1, const char *string)
get_subseq_F
double get_subseq_F(int i, int j)
Get the free energy of a subsequence from the q[] array.
data_structures.h
update_pf_params_par
void update_pf_params_par(int length, vrna_exp_param_t *parameters)
Recalculate energy parameters.
init_pf_fold
void init_pf_fold(int length)
Allocate space for pf_fold()
st_back
int st_back
Flag indicating that auxilary arrays are needed throughout the computations. This is essential for st...
centroid
char * centroid(int length, double *dist)
vrna_pf
float vrna_pf(vrna_fold_compound_t *vc, char *structure)
Compute the partition function for a given RNA sequence, or sequence alignment.
pf_fold
float pf_fold(const char *sequence, char *structure)
Compute the partition function of an RNA sequence.
export_bppm
FLT_OR_DBL * export_bppm(void)
Get a pointer to the base pair probability arrayAccessing the base pair probabilities for a pair (i...
params.h
vrna_exp_param_s
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
boltzmann_sampling.h
Boltzmann Sampling of secondary structures from the ensemble.
free_pf_arrays
void free_pf_arrays(void)
Free arrays for the partition function recursions.
vrna_pf_circfold
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...
mean_bp_distance
double mean_bp_distance(int length)
Get the mean base pair distance of the last partition function computation.
vrna_pf_fold
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...
vrna_plist_s
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:164
pbacktrack_circ
char * pbacktrack_circ(char *sequence)
Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability...
update_pf_params
void update_pf_params(int length)
Recalculate energy parameters.
mean_bp_distance_pr
double mean_bp_distance_pr(int length, FLT_OR_DBL *pr)
Get the mean base pair distance in the thermodynamic ensemble.
pr
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
get_pf_arrays
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...
pbacktrack
char * pbacktrack(char *sequence)
Sample a secondary structure from the Boltzmann ensemble according its probability.
stackProb
vrna_plist_t * stackProb(double cutoff)
Get the probability of stacks.
pf_fold_par
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.
expLoopEnergy
double expLoopEnergy(int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)
vrna_pf_float_precision
int vrna_pf_float_precision(void)
Find out whether partition function computations are using single precision floating points...
mean_bp_dist
double mean_bp_dist(int length)
centroid.h
Centroid structure computation.