Heuristics for two-step pseudoknot forming interaction predictions. More...
Go to the source code of this file.
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_t * | vrna_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... | |
Heuristics for two-step pseudoknot forming interaction predictions.