RNAlib-2.6.0a
pk_plex.h
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1#ifndef VIENNA_RNA_PACKAGE_PK_PLEX_H
2#define VIENNA_RNA_PACKAGE_PK_PLEX_H
3
4#ifdef VRNA_WARN_DEPRECATED
5# if defined(DEPRECATED)
6# undef DEPRECATED
7# endif
8# if defined(__clang__)
9# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
10# elif defined(__GNUC__)
11# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
12# else
13# define DEPRECATED(func, msg) func
14# endif
15#else
16# define DEPRECATED(func, msg) func
17#endif
18
60typedef int (*vrna_pk_plex_score_f)(const short *pt,
61 int start_5,
62 int end_5,
63 int start_3,
64 int end_3,
65 void *data);
66
67DEPRECATED(typedef int (vrna_callback_pk_plex_score)(const short *pt,
68 int start_5,
69 int end_5,
70 int start_3,
71 int end_3,
72 void *data),
73 "Use vrna_pk_plex_score_f instead!");
74
75
82typedef struct vrna_pk_plex_option_s *vrna_pk_plex_opt_t;
83
90
92
99 char *structure;
100 double energy;
101 double dGpk;
102 double dGint;
103 double dG1;
104 double dG2;
105 unsigned int start_5;
106 unsigned int end_5;
107 unsigned int start_3;
108 unsigned int end_3;
109};
110
142 const int **accessibility,
143 vrna_pk_plex_opt_t options);
144
145
156int **
157vrna_pk_plex_accessibility(const char *sequence,
158 unsigned int unpaired,
159 double cutoff);
160
161
171
172
184vrna_pk_plex_opt(unsigned int delta,
185 unsigned int max_interaction_length,
186 int pk_penalty);
187
188
201vrna_pk_plex_opt_fun(unsigned int delta,
202 unsigned int max_interaction_length,
203 vrna_pk_plex_score_f scoring_function,
204 void *scoring_data);
205
206
211#endif
The Basic Fold Compound API.
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:156
double energy
Net free energy in kcal/mol.
Definition: pk_plex.h:100
char * structure
Secondary Structure in dot-bracket notation.
Definition: pk_plex.h:99
unsigned int start_3
Start coordinate of the 3' interaction site.
Definition: pk_plex.h:107
double dG2
Opening energy for the 3' interaction site used in the heuristic.
Definition: pk_plex.h:104
unsigned int end_3
End coordinate of the 3' interaction site.
Definition: pk_plex.h:108
double dGint
Free energy of PK forming duplex interaction.
Definition: pk_plex.h:102
double dGpk
Free energy of PK loop in kcal/mol.
Definition: pk_plex.h:101
double dG1
Opening energy for the 5' interaction site used in the heuristic.
Definition: pk_plex.h:103
unsigned int end_5
End coordinate of the 5' interaction site.
Definition: pk_plex.h:106
unsigned int start_5
Start coordinate of the 5' interaction site.
Definition: pk_plex.h:105
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:60
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:82
A result of the RNA PKplex interaction prediction.
Definition: pk_plex.h:98
int unpaired
contains the number of unpaired bases.