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_pk_plex_score_f) (const short *pt, int start_5, int end_5, int start_3, int end_3, void *data) |
Pseudoknot loop scoring function prototype. | |
typedef struct vrna_pk_plex_option_s * | vrna_pk_plex_opt_t |
RNA PKplex options object. | |
typedef struct vrna_pk_plex_result_s | vrna_pk_plex_t |
Convenience typedef for results of the RNA PKplex prediction. | |
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. | |
int ** | vrna_pk_plex_accessibility (const char *sequence, unsigned int unpaired, double cutoff) |
Obtain a list of opening energies suitable for PKplex computations. | |
vrna_pk_plex_opt_t | vrna_pk_plex_opt_defaults (void) |
Default options for PKplex algorithm. | |
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. | |
vrna_pk_plex_opt_t | vrna_pk_plex_opt_fun (unsigned int delta, unsigned int max_interaction_length, vrna_pk_plex_score_f scoring_function, void *scoring_data) |
Simple options for PKplex algorithm. | |
Heuristics for two-step pseudoknot forming interaction predictions.