1#ifndef VIENNA_RNA_PACKAGE_PK_PLEX_H
2#define VIENNA_RNA_PACKAGE_PK_PLEX_H
4#ifdef VRNA_WARN_DEPRECATED
5# if defined(DEPRECATED)
9# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
10# elif defined(__GNUC__)
11# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
13# define DEPRECATED(func, msg) func
16# define DEPRECATED(func, msg) func
68DEPRECATED(
typedef int (vrna_callback_pk_plex_score)(
const short *pt,
74 "Use vrna_pk_plex_score_f instead!");
143 const int **accessibility,
186 unsigned int max_interaction_length,
203 unsigned int max_interaction_length,
The Basic Fold Compound API.
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:168
double energy
Net free energy in kcal/mol.
Definition pk_plex.h:101
char * structure
Secondary Structure in dot-bracket notation.
Definition pk_plex.h:100
unsigned int start_3
Start coordinate of the 3' interaction site.
Definition pk_plex.h:108
double dG2
Opening energy for the 3' interaction site used in the heuristic.
Definition pk_plex.h:105
unsigned int end_3
End coordinate of the 3' interaction site.
Definition pk_plex.h:109
double dGint
Free energy of PK forming duplex interaction.
Definition pk_plex.h:103
double dGpk
Free energy of PK loop in kcal/mol.
Definition pk_plex.h:102
double dG1
Opening energy for the 5' interaction site used in the heuristic.
Definition pk_plex.h:104
unsigned int end_5
End coordinate of the 5' interaction site.
Definition pk_plex.h:107
unsigned int start_5
Start coordinate of the 5' interaction site.
Definition pk_plex.h:106
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.
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.
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.
int ** vrna_pk_plex_accessibility(const char *sequence, unsigned int unpaired, double cutoff)
Obtain a list of opening energies suitable for PKplex computations.
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.
Definition pk_plex.h:61
vrna_pk_plex_opt_t vrna_pk_plex_opt_defaults(void)
Default options for PKplex algorithm.
struct vrna_pk_plex_option_s * vrna_pk_plex_opt_t
RNA PKplex options object.
Definition pk_plex.h:83
A result of the RNA PKplex interaction prediction.
Definition pk_plex.h:99
int unpaired
contains the number of unpaired bases.