1 #ifndef VIENNA_RNA_PACKAGE_LPFOLD_H 2 #define VIENNA_RNA_PACKAGE_LPFOLD_H 4 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 20 #ifdef VRNA_WARN_DEPRECATED 21 # if defined(__clang__) 22 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg))) 23 # elif defined(__GNUC__) 24 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg))) 26 # define DEPRECATED(func, msg) func 29 # define DEPRECATED(func, msg) func 40 "This function is obsolete");
49 DEPRECATED(
void update_pf_paramsLP_par(
int length,
51 "Use the new API with vrna_folc_compound_t instead");
99 "Use vrna_pfl_fold(), vrna_pfl_fold_cb(), vrna_pfl_fold_up(), or vrna_pfl_fold_up_cb() instead");
117 "Use the new API and vrna_probs_window() instead");
120 DEPRECATED(
void putoutpU_prob_par(
double **pU,
151 DEPRECATED(
void putoutpU_prob_bin_par(
double **pU,
188 "This function is obsolete");
void update_pf_paramsLP(int length)
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.
Various data structures and pre-processor macros.
void init_pf_foldLP(int length)
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: basic.h:101
Functions to deal with sets of energy parameters.
void putoutpU_prob(double **pU, int length, int ulength, FILE *fp, int energies)
Writes the unpaired probabilities (pU) or opening energies into a 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.
Partition function and equilibrium probability implementation for the sliding window algorithm...
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.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:358