1 #ifndef VIENNA_RNA_PACKAGE_ALIFOLD_H
2 #define VIENNA_RNA_PACKAGE_ALIFOLD_H
5 #define VRNA_BACKWARD_COMPAT
15 #ifdef DEPRECATION_WARNINGS
17 # define DEPRECATED(func) func __attribute__ ((deprecated))
19 # define DEPRECATED(func) func
22 # define DEPRECATED(func) func
185 #ifdef VRNA_BACKWARD_COMPAT
214 DEPRECATED(
float alifold(
const char **strings,
char *structure));
229 DEPRECATED(
float circalifold(
const char **strings,
char *structure));
261 DEPRECATED(
float energy_of_alistruct(
const char **sequences,
const char *structure,
int n_seq,
float *energy));
263 DEPRECATED(
float energy_of_ali_gquad_structure(
const char **sequences,
const char *structure,
int n_seq,
float *energy));
275 DEPRECATED(
extern double cv_fact);
286 DEPRECATED(
extern double nc_fact);
421 unsigned short ***a2s_p,
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 ...
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...
float alifold(const char **strings, char *structure)
Compute MFE and according consensus structure of an alignment of sequences.
FLT_OR_DBL * export_ali_bppm(void)
Get a pointer to the base pair probability array.
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:39
void update_alifold_params(void)
Update the energy parameters for alifold function.
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
float vrna_circalifold(const char **ssequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for a sequence a...
void free_alifold_arrays(void)
Free the memory occupied by MFE alifold functions.
float circalifold(const char **strings, char *structure)
Compute MFE and according structure of an alignment of sequences assuming the sequences are circular ...
char * alipbacktrack(double *prob)
Sample a consensus secondary structure from the Boltzmann ensemble according its probability.
void free_alipf_arrays(void)
Free the memory occupied by folding matrices allocated by alipf_fold, alipf_circ_fold, etc.
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
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 of secondary structures from the ensemble.
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...
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...
Various utility- and helper-functions for sequence alignments and comparative structure prediction...
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:164
Partition function of single RNA sequences.
float alipf_circ_fold(const char **sequences, char *structure, vrna_plist_t **pl)
MFE calculations for single RNA sequences.
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.
float vrna_alifold(const char **ssequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for an RNA seque...
Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.