RNAlib-2.6.3
 
Loading...
Searching...
No Matches
pk_plex.h
Go to the documentation of this file.
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
61typedef int (*vrna_pk_plex_score_f)(const short *pt,
62 int start_5,
63 int end_5,
64 int start_3,
65 int end_3,
66 void *data);
67
68DEPRECATED(typedef int (vrna_callback_pk_plex_score)(const short *pt,
69 int start_5,
70 int end_5,
71 int start_3,
72 int end_3,
73 void *data),
74 "Use vrna_pk_plex_score_f instead!");
75
76
83typedef struct vrna_pk_plex_option_s *vrna_pk_plex_opt_t;
84
91
93
100 char *structure;
101 double energy;
102 double dGpk;
103 double dGint;
104 double dG1;
105 double dG2;
106 unsigned int start_5;
107 unsigned int end_5;
108 unsigned int start_3;
109 unsigned int end_3;
110};
111
143 const int **accessibility,
144 vrna_pk_plex_opt_t options);
145
146
157int **
158vrna_pk_plex_accessibility(const char *sequence,
159 unsigned int unpaired,
160 double cutoff);
161
162
172
173
185vrna_pk_plex_opt(unsigned int delta,
186 unsigned int max_interaction_length,
187 int pk_penalty);
188
189
202vrna_pk_plex_opt_fun(unsigned int delta,
203 unsigned int max_interaction_length,
204 vrna_pk_plex_score_f scoring_function,
205 void *scoring_data);
206
207
212#endif
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.