RNAlib-2.4.5
LPfold.h File Reference

Partition function implementation for the Lfold algorithm. More...

+ Include dependency graph for LPfold.h:

Go to the source code of this file.

Macros

#define VRNA_PROBS_WINDOW_BPP   4096U
 Option flag to activate callback triggers for pairing probabilities. More...
 
#define VRNA_PROBS_WINDOW_UP   8192U
 Option flag to activate callback triggers for unpaired probabilities. More...
 
#define VRNA_PROBS_WINDOW_STACKP   16384U
 Option flag to activate callback triggers for stacking probabilities. More...
 
#define VRNA_PROBS_WINDOW_UP_SPLIT   32768U
 Option flag to activate callback triggers for unpaired probabilities (split up into different loop types) More...
 

Typedefs

typedef 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. More...
 

Functions

vrna_ep_tvrna_pfl_fold (const char *sequence, int window_size, int max_bp_span, float cutoff)
 Compute base pair probabilities using a sliding-window approach. More...
 
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) More...
 
double ** vrna_pfl_fold_up (const char *sequence, int ulength, int window_size, int max_bp_span)
 Compute probability of contiguous unpaired segments. More...
 
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. More...
 
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. More...
 
void update_pf_paramsLP (int length)
 
vrna_ep_tpfl_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. More...
 
vrna_ep_tpfl_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.
 
void putoutpU_prob (double **pU, int length, int ulength, FILE *fp, int energies)
 Writes the unpaired probabilities (pU) or opening energies into a file. More...
 
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. More...
 
void init_pf_foldLP (int length)
 

Detailed Description

Partition function implementation for the Lfold algorithm.

Typedef Documentation

◆ vrna_probs_window_callback

typedef 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.

Notes on Callback Functions:
This function will be called for each probability data set in the sliding window probability computation implementation of vrna_probs_window(). The argument type specifies the type of probability that is passed to this function.
See also
vrna_probs_window(), vrna_pfl_fold_up_cb() VRNA_PROBS_WINDOW_BPP, VRNA_PROBS_WINDOW_UP, VRNA_PROBS_WINDOW_STACKP, #VRNA_EXT_LOOP, #VRNA_HP_LOOP, #VRNA_INT_LOOP, #VRNA_MB_LOOP, #VRNA_ANY_LOOP
Parameters
prAn array of probabilities
pr_sizeThe length of the probability array
iThe i-position (5') of the probabilities
maxThe (theoretical) maximum length of the probability array
dataAuxiliary data

Function Documentation

◆ init_pf_foldLP()

void init_pf_foldLP ( int  length)

Dunno if this function was ever used by external programs linking to RNAlib, but it was declared PUBLIC before. Anyway, never use this function as it will be removed soon and does nothing at all