RNAlib-2.5.1

Heuristics for two-step pseudoknot forming interaction predictions. More...

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Data Structures

struct  vrna_pk_plex_result_s
 A result of the RNA PKplex interaction prediction. More...
 

Typedefs

typedef int() vrna_callback_pk_plex_score(const short *pt, int start_5, int end_5, int start_3, int end_3, void *data)
 Pseudoknot loop scoring function prototype. More...
 
typedef struct vrna_pk_plex_option_s * vrna_pk_plex_opt_t
 RNA PKplex options object. More...
 
typedef struct vrna_pk_plex_result_s vrna_pk_plex_t
 Convenience typedef for results of the RNA PKplex prediction. More...
 

Functions

vrna_pk_plex_tvrna_pk_plex (vrna_fold_compound_t *fc, const int **accessibility, vrna_pk_plex_opt_t options)
 Predict Pseudoknot interactions in terms of a two-step folding process. More...
 
int ** vrna_pk_plex_accessibility (const char *sequence, unsigned int unpaired, double cutoff)
 Obtain a list of opening energies suitable for PKplex computations. More...
 
vrna_pk_plex_opt_t vrna_pk_plex_opt_defaults (void)
 Default options for PKplex algorithm. More...
 
vrna_pk_plex_opt_t vrna_pk_plex_opt (unsigned int delta, unsigned int max_interaction_length, int pk_penalty)
 Simple options for PKplex algorithm. More...
 
vrna_pk_plex_opt_t vrna_pk_plex_opt_fun (unsigned int delta, unsigned int max_interaction_length, vrna_callback_pk_plex_score *scoring_function, void *scoring_data)
 Simple options for PKplex algorithm. More...
 

Detailed Description

Heuristics for two-step pseudoknot forming interaction predictions.