1 #ifndef VIENNA_RNA_PACKAGE_LPFOLD_H 2 #define VIENNA_RNA_PACKAGE_LPFOLD_H 44 #ifdef VRNA_WARN_DEPRECATED 45 # if defined(__clang__) 46 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg))) 47 # elif defined(__GNUC__) 48 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg))) 50 # define DEPRECATED(func, msg) func 53 # define DEPRECATED(func, msg) func 57 #define VRNA_EXT_LOOP 1U 58 #define VRNA_HP_LOOP 2U 59 #define VRNA_INT_LOOP 4U 60 #define VRNA_MB_LOOP 8U 61 #define VRNA_ANY_LOOP (VRNA_EXT_LOOP | VRNA_HP_LOOP | VRNA_INT_LOOP | VRNA_MB_LOOP) 69 #define VRNA_PROBS_WINDOW_BPP 4096U 76 #define VRNA_PROBS_WINDOW_UP 8192U 83 #define VRNA_PROBS_WINDOW_STACKP 16384U 90 #define VRNA_PROBS_WINDOW_UP_SPLIT 32768U 93 #define VRNA_PROBS_WINDOW_PF 65536U 231 unsigned int options,
236 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 246 "This function is obsolete");
255 DEPRECATED(
void update_pf_paramsLP_par(
int length,
257 "Use the new API with vrna_folc_compound_t instead");
305 "Use vrna_pfl_fold(), vrna_pfl_fold_cb(), vrna_pfl_fold_up(), or vrna_pfl_fold_up_cb() instead");
323 "Use the new API and vrna_probs_window() instead");
326 DEPRECATED(
void putoutpU_prob_par(
double **pU,
357 DEPRECATED(
void putoutpU_prob_bin_par(
double **pU,
394 "This function is obsolete");
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(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: structure_utils.h:114
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:43
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:131
void vrna_pfl_fold_up_cb(const char *sequence, int ulength, int window_size, int max_bp_span, vrna_probs_window_callback *cb, void *data)
Compute probability of contiguous unpaired segments.
vrna_ep_t * vrna_pfl_fold(const char *sequence, int window_size, int max_bp_span, float cutoff)
Compute base pair probabilities using a sliding-window approach.
Various data structures and pre-processor macros.
void() vrna_probs_window_callback(FLT_OR_DBL *pr, int pr_size, int i, int max, unsigned int type, void *data)
Sliding window probability computation callback.
Definition: LPfold.h:34
void init_pf_foldLP(int length)
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.
Functions to deal with sets of energy parameters.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:101
void update_pf_paramsLP(int length)
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 vrna_pfl_fold_cb(const char *sequence, int window_size, int max_bp_span, vrna_probs_window_callback *cb, void *data)
Compute base pair probabilities using a sliding-window approach (callback version) ...
double ** vrna_pfl_fold_up(const char *sequence, int ulength, int window_size, int max_bp_span)
Compute probability of contiguous unpaired segments.
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
int max_bp_span
Maximum allowed base pair span.
void vrna_probs_window(vrna_fold_compound_t *fc, int ulength, unsigned int options, vrna_probs_window_callback *cb, void *data)
Compute various equilibrium probabilities under a sliding window approach.