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alifold.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_ALIFOLD_H
2 #define VIENNA_RNA_PACKAGE_ALIFOLD_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/ribo.h>
10 #include <ViennaRNA/mfe.h>
11 #include <ViennaRNA/part_func.h>
12 #include <ViennaRNA/aln_util.h>
13 #include <ViennaRNA/boltzmann_sampling.h>
14
15 #ifdef DEPRECATION_WARNINGS
16 # ifdef __GNUC__
17 # define DEPRECATED(func) func __attribute__ ((deprecated))
18 # else
19 # define DEPRECATED(func) func
20 # endif
21 #else
22 # define DEPRECATED(func) func
23 #endif
24
54 /*
55 ##############################################
56 # MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION #
57 ##############################################
58 */
59
83 float
84 vrna_alifold( const char **sequences,
85 char *structure);
86
113 float
114 vrna_circalifold( const char **sequences,
115 char *structure);
116
117 /*
118 #############################################################
119 # PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION #
120 #############################################################
121 */
122
123
155 float vrna_pf_alifold(const char **sequences, char *structure, vrna_plist_t **pl);
156
183 float vrna_pf_circalifold(const char **sequences, char *structure, vrna_plist_t **pl);
184
185 #ifdef VRNA_BACKWARD_COMPAT
186
187 /*
188 #################################################
189 # DEPRECATED FUNCTIONS #
190 #################################################
191 */
192
193
214 DEPRECATED(float alifold( const char **strings, char *structure));
215
229 DEPRECATED(float circalifold( const char **strings, char *structure));
230
244 DEPRECATED(void free_alifold_arrays(void));
245
261 DEPRECATED(float energy_of_alistruct(const char **sequences, const char *structure, int n_seq, float *energy));
262
263 DEPRECATED(float energy_of_ali_gquad_structure(const char **sequences, const char *structure, int n_seq, float *energy));
264
275 DEPRECATED(extern double cv_fact);
286 DEPRECATED(extern double nc_fact);
287
304 DEPRECATED(float alipf_fold_par( const char **sequences,
305 char *structure,
306 vrna_plist_t **pl,
307 vrna_exp_param_t *parameters,
308 int calculate_bppm,
309 int is_constrained,
310 int is_circular));
311
330 DEPRECATED(float alipf_fold( const char **sequences, char *structure, vrna_plist_t **pl));
331
344 DEPRECATED(float alipf_circ_fold(const char **sequences, char *structure, vrna_plist_t **pl));
345
346
365 DEPRECATED(FLT_OR_DBL *export_ali_bppm(void));
366
379 DEPRECATED(void free_alipf_arrays(void));
380
391 DEPRECATED(char *alipbacktrack(double *prob));
392
419 DEPRECATED(int get_alipf_arrays(short ***S_p,
420 short ***S5_p,
421 short ***S3_p,
422 unsigned short ***a2s_p,
423 char ***Ss_p,
424 FLT_OR_DBL **qb_p,
425 FLT_OR_DBL **qm_p,
426 FLT_OR_DBL **q1k_p,
427 FLT_OR_DBL **qln_p,
428 short **pscore));
429
430
442 DEPRECATED(void update_alifold_params(void));
443
444 #endif
445
446
447 #endif
vrna_pf_circalifold
float vrna_pf_circalifold(const char **sequences, char *structure, vrna_plist_t **pl)
Compute Partition function (and base pair probabilities) for an alignment of circular RNA sequences ...
vrna_pf_alifold
float vrna_pf_alifold(const char **sequences, char *structure, vrna_plist_t **pl)
Compute Partition function (and base pair probabilities) for an RNA sequence alignment using a compa...
get_alipf_arrays
int get_alipf_arrays(short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, FLT_OR_DBL **qb_p, FLT_OR_DBL **qm_p, FLT_OR_DBL **q1k_p, FLT_OR_DBL **qln_p, short **pscore)
Get pointers to (almost) all relavant arrays used in alifold&#39;s partition function computation...
alifold
float alifold(const char **strings, char *structure)
Compute MFE and according consensus structure of an alignment of sequences.
export_ali_bppm
FLT_OR_DBL * export_ali_bppm(void)
Get a pointer to the base pair probability array.
cv_fact
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
FLT_OR_DBL
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:39
update_alifold_params
void update_alifold_params(void)
Update the energy parameters for alifold function.
nc_fact
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
free_alifold_arrays
void free_alifold_arrays(void)
Free the memory occupied by MFE alifold functions.
circalifold
float circalifold(const char **strings, char *structure)
Compute MFE and according structure of an alignment of sequences assuming the sequences are circular ...
data_structures.h
alipbacktrack
char * alipbacktrack(double *prob)
Sample a consensus secondary structure from the Boltzmann ensemble according its probability.
free_alipf_arrays
void free_alipf_arrays(void)
Free the memory occupied by folding matrices allocated by alipf_fold, alipf_circ_fold, etc.
params.h
vrna_alifold
float vrna_alifold(const char **sequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for an RNA seque...
vrna_exp_param_s
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
vrna_circalifold
float vrna_circalifold(const char **sequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for a sequence a...
alipf_fold_par
float alipf_fold_par(const char **sequences, char *structure, vrna_plist_t **pl, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained, int is_circular)
boltzmann_sampling.h
Boltzmann Sampling of secondary structures from the ensemble.
alipf_fold
float alipf_fold(const char **sequences, char *structure, vrna_plist_t **pl)
The partition function version of alifold() works in analogy to pf_fold(). Pair probabilities and inf...
aln_util.h
Various utility- and helper-functions for sequence alignments and comparative structure prediction...
vrna_plist_s
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:164
part_func.h
Partition function of single RNA sequences.
alipf_circ_fold
float alipf_circ_fold(const char **sequences, char *structure, vrna_plist_t **pl)
mfe.h
MFE calculations for single RNA sequences.
energy_of_alistruct
float energy_of_alistruct(const char **sequences, const char *structure, int n_seq, float *energy)
Calculate the free energy of a consensus structure given a set of aligned sequences.
ribo.h
Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.