alifold.h
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#ifndef VIENNA_RNA_PACKAGE_ALIFOLD_H
#define VIENNA_RNA_PACKAGE_ALIFOLD_H
/* make this interface backward compatible with RNAlib < 2.2.0 */
#define VRNA_BACKWARD_COMPAT
#include <ViennaRNA/data_structures.h>
#include <ViennaRNA/params.h>
#include <ViennaRNA/ribo.h>
#include <ViennaRNA/mfe.h>
#include <ViennaRNA/part_func.h>
#include <ViennaRNA/aln_util.h>
#include <ViennaRNA/boltzmann_sampling.h>
#ifdef DEPRECATION_WARNINGS
# ifdef __GNUC__
# define DEPRECATED(func) func __attribute__ ((deprecated))
# else
# define DEPRECATED(func) func
# endif
#else
# define DEPRECATED(func) func
#endif
/*
##############################################
# MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION #
##############################################
*/
float
vrna_alifold( const char **ssequences,
char *structure);
float
vrna_circalifold( const char **ssequences,
char *structure);
/*
#############################################################
# PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION #
#############################################################
*/
float vrna_pf_alifold(const char **strings, char *structure, vrna_plist_t **pl);
float vrna_pf_circalifold(const char **sequences, char *structure, vrna_plist_t **pl);
#ifdef VRNA_BACKWARD_COMPAT
/*
#################################################
# DEPRECATED FUNCTIONS #
#################################################
*/
DEPRECATED(float alifold( const char **strings, char *structure));
DEPRECATED(float circalifold( const char **strings, char *structure));
DEPRECATED(void free_alifold_arrays(void));
DEPRECATED(float energy_of_alistruct(const char **sequences, const char *structure, int n_seq, float *energy));
DEPRECATED(float energy_of_ali_gquad_structure(const char **sequences, const char *structure, int n_seq, float *energy));
DEPRECATED(extern double cv_fact);
DEPRECATED(extern double nc_fact);
DEPRECATED(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));
DEPRECATED(float alipf_fold( const char **sequences, char *structure, vrna_plist_t **pl));
DEPRECATED(float alipf_circ_fold(const char **sequences, char *structure, vrna_plist_t **pl));
DEPRECATED(FLT_OR_DBL *export_ali_bppm(void));
DEPRECATED(void free_alipf_arrays(void));
DEPRECATED(char *alipbacktrack(double *prob));
DEPRECATED(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));
DEPRECATED(void update_alifold_params(void));
#endif
#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 ...
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'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...
vrna_circalifold
float vrna_circalifold(const char **ssequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for a sequence a...
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_exp_param_s
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
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...
vrna_pf_alifold
float vrna_pf_alifold(const char **strings, char *structure, vrna_plist_t **pl)
Compute Partition function (and base pair probabilities) for an RNA sequence alignment using a compa...
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.
vrna_alifold
float vrna_alifold(const char **ssequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for an RNA seque...
ribo.h
Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.