1#ifndef VIENNA_RNA_PACKAGE_LPFOLD_H
2#define VIENNA_RNA_PACKAGE_LPFOLD_H
4#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
22#ifdef VRNA_WARN_DEPRECATED
23# if defined(__clang__)
24# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
25# elif defined(__GNUC__)
26# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
28# define DEPRECATED(func, msg) func
31# define DEPRECATED(func, msg) func
42"This function is obsolete");
51DEPRECATED(
void update_pf_paramsLP_par(
int length,
53"Use the new API with vrna_folc_compound_t instead");
101"Use vrna_pfl_fold(), vrna_pfl_fold_cb(), vrna_pfl_fold_up(), or vrna_pfl_fold_up_cb() instead");
119"Use the new API and vrna_probs_window() instead");
122DEPRECATED(
void putoutpU_prob_par(
double **pU,
153DEPRECATED(
void putoutpU_prob_bin_par(
double **pU,
190"This function is obsolete");
void init_pf_foldLP(int length)
Various data structures and pre-processor macros.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition: basic.h:103
void putoutpU_prob(double **pU, int length, int ulength, FILE *fp, int energies)
Writes the unpaired probabilities (pU) or opening energies into a file.
void update_pf_paramsLP(int length)
void putoutpU_prob_bin(double **pU, int length, int ulength, FILE *fp, int energies)
Writes the unpaired probabilities (pU) or opening energies into a binary file.
vrna_ep_t * pfl_fold_par(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, vrna_ep_t **dpp2, FILE *pUfp, FILE *spup, vrna_exp_param_t *parameters)
Compute partition functions for locally stable secondary structures.
vrna_ep_t * pfl_fold(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, vrna_ep_t **dpp2, FILE *pUfp, FILE *spup)
Compute partition functions for locally stable secondary structures.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:482
Functions to deal with sets of energy parameters.
Partition function and equilibrium probability implementation for the sliding window algorithm.