RNAlib-2.6.3
 
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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_result_f)(const char *stucture,
49 float energy,
50 void *data);
51
52DEPRECATED(typedef void (vrna_subopt_callback)(const char *stucture,
53 float energy,
54 void *data),
55 "Use vrna_subopt_result_f instead!");
56
57#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
58
64
65#endif
66
67#include <stdio.h>
68
72
73
78 float energy;
79 char *structure;
80};
81
85#define MAXDOS 1000
86
94#define VRNA_UNSORTED 0
95#define VRNA_SORT_BY_ENERGY_LEXICOGRAPHIC_ASC 1
96#define VRNA_SORT_BY_ENERGY_ASC 2
97
131 int delta,
132 int sorted,
133 FILE *fp);
134
135
171void
173 int delta,
175 void *data);
176
177
184extern double print_energy;
185
192extern int subopt_sorted;
193
211extern int density_of_states[MAXDOS + 1];
212 /* End of group dos */
214
215#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
216
234DEPRECATED(SOLUTION * subopt(char *seq, char *structure, int delta, FILE * fp),
235 "Use vrna_subopt() or vrna_subopt_cb() instead");
236
242DEPRECATED(SOLUTION *
243 subopt_par(char *seq, char *structure, vrna_param_t * parameters, int delta,
244 int is_constrained,
245 int is_circular, FILE * fp),
246 "Use vrna_subopt() or vrna_subopt_cb() instead");
247
262DEPRECATED(SOLUTION * subopt_circ(char *seq, char *sequence, int delta, FILE * fp),
263 "Use vrna_subopt() or vrna_subopt_cb() instead");
264
279DEPRECATED(SOLUTION * zukersubopt(const char *string),
280 "Use vrna_subopt_zuker() instead");
281
290DEPRECATED(SOLUTION * zukersubopt_par(const char *string, vrna_param_t * parameters),
291 "Use vrna_subopt_zuker() instead");
292
293
294#endif
295
296#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:168
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.
void(* vrna_subopt_result_f)(const char *stucture, float energy, void *data)
Callback for vrna_subopt_cb()
Definition subopt.h:48
int subopt_sorted
Sort output by energy.
void vrna_subopt_cb(vrna_fold_compound_t *fc, int delta, vrna_subopt_result_f cb, void *data)
Generate suboptimal structures within an energy band arround the MFE.
SOLUTION * subopt(char *seq, char *structure, int delta, FILE *fp)
Returns list of subopt structures or writes to fp.
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:77
char * structure
Structure in dot-bracket notation.
Definition subopt.h:79
float energy
Free Energy of structure in kcal/mol.
Definition subopt.h:78
#define MAXDOS
Maximum density of states discretization for subopt.
Definition subopt.h:85