RNAlib-2.5.1
subopt.h
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1/* subopt.h */
2#ifndef VIENNA_RNA_PACKAGE_SUBOPT_H
3#define VIENNA_RNA_PACKAGE_SUBOPT_H
4
5#ifdef VRNA_WARN_DEPRECATED
6# if defined(__clang__)
7# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
8# elif defined(__GNUC__)
9# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
10# else
11# define DEPRECATED(func, msg) func
12# endif
13#else
14# define DEPRECATED(func, msg) func
15#endif
16
32
48typedef void (vrna_subopt_callback)(const char *stucture,
49 float energy,
50 void *data);
51
52#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
53
59
60#endif
61
62#include <stdio.h>
63
67
68
73 float energy;
74 char *structure;
75};
76
80#define MAXDOS 1000
81
89#define VRNA_UNSORTED 0
90#define VRNA_SORT_BY_ENERGY_LEXICOGRAPHIC_ASC 1
91#define VRNA_SORT_BY_ENERGY_ASC 2
92
125 int delta,
126 int sorted,
127 FILE *fp);
128
129
164void
166 int delta,
168 void *data);
169
170
177extern double print_energy;
178
185extern int subopt_sorted;
186
203extern int density_of_states[MAXDOS + 1];
204 /* End of group dos */
206
207#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
208
226DEPRECATED(SOLUTION * subopt(char *seq, char *structure, int delta, FILE * fp),
227 "Use vrna_subopt() or vrna_subopt_cb() instead");
228
234DEPRECATED(SOLUTION *
235 subopt_par(char *seq, char *structure, vrna_param_t * parameters, int delta,
236 int is_constrained,
237 int is_circular, FILE * fp),
238 "Use vrna_subopt() or vrna_subopt_cb() instead");
239
254DEPRECATED(SOLUTION * subopt_circ(char *seq, char *sequence, int delta, FILE * fp),
255 "Use vrna_subopt() or vrna_subopt_cb() instead");
256
271DEPRECATED(SOLUTION * zukersubopt(const char *string),
272 "Use vrna_subopt_zuker() instead");
273
282DEPRECATED(SOLUTION * zukersubopt_par(const char *string, vrna_param_t * parameters),
283 "Use vrna_subopt_zuker() instead");
284
285
286#endif
287
288#endif
Various data structures and pre-processor macros.
The Basic Fold Compound API.
int density_of_states[MAXDOS+1]
The Density of States.
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:148
double print_energy
printing threshold for use with logML
SOLUTION * subopt_circ(char *seq, char *sequence, int delta, FILE *fp)
Returns list of circular subopt structures or writes to fp.
int subopt_sorted
Sort output by energy.
SOLUTION * subopt(char *seq, char *structure, int delta, FILE *fp)
Returns list of subopt structures or writes to fp.
void() vrna_subopt_callback(const char *stucture, float energy, void *data)
Callback for vrna_subopt_cb()
Definition: subopt.h:48
void vrna_subopt_cb(vrna_fold_compound_t *fc, int delta, vrna_subopt_callback *cb, void *data)
Generate suboptimal structures within an energy band arround the MFE.
vrna_subopt_solution_t * vrna_subopt(vrna_fold_compound_t *fc, int delta, int sorted, FILE *fp)
Returns list of subopt structures or writes to fp.
SOLUTION * subopt_par(char *seq, char *structure, vrna_param_t *parameters, int delta, int is_constrained, int is_circular, FILE *fp)
Returns list of subopt structures or writes to fp.
SOLUTION * zukersubopt(const char *string)
Compute Zuker type suboptimal structures.
SOLUTION * zukersubopt_par(const char *string, vrna_param_t *parameters)
Compute Zuker type suboptimal structures.
Functions to deal with sets of energy parameters.
Solution element from subopt.c.
Definition: subopt.h:72
char * structure
Structure in dot-bracket notation.
Definition: subopt.h:74
float energy
Free Energy of structure in kcal/mol.
Definition: subopt.h:73
#define MAXDOS
Maximum density of states discretization for subopt.
Definition: subopt.h:80