RNAlib-2.3.1
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 DEPRECATION_WARNINGS
6 # ifdef __GNUC__
7 # define DEPRECATED(func) func __attribute__ ((deprecated))
8 # else
9 # define DEPRECATED(func) func
10 # endif
11 #else
12 # define DEPRECATED(func) func
13 #endif
14 
21 #define VRNA_BACKWARD_COMPAT
22 
27 
32 typedef void (vrna_subopt_callback)(const char *stucture, float energy, void *data);
33 
34 #ifdef VRNA_BACKWARD_COMPAT
35 
40 typedef struct vrna_subopt_sol_s SOLUTION;
41 
42 #endif
43 
45 #include <ViennaRNA/params.h>
46 
47 
52  float energy;
53  char *structure;
54 };
55 
59 #define MAXDOS 1000
60 
100  int delta,
101  int sorted,
102  FILE *fp);
103 
138 void
140  int delta,
142  void *data);
143 
170 
177 extern double print_energy;
178 
185 extern int subopt_sorted;
186 
203 extern int density_of_states[MAXDOS+1];
204  /* End of group dos */
206 
207 #ifdef VRNA_BACKWARD_COMPAT
208 
226 DEPRECATED(SOLUTION *subopt (char *seq, char *structure, int delta, FILE *fp));
227 
233 DEPRECATED(SOLUTION *subopt_par(char *seq, char *structure, vrna_param_t *parameters, int delta, int is_constrained, int is_circular, FILE *fp));
234 
249 DEPRECATED(SOLUTION *subopt_circ(char *seq, char *sequence, int delta, FILE *fp));
250 
265 DEPRECATED(SOLUTION *zukersubopt(const char *string));
266 
275 DEPRECATED(SOLUTION *zukersubopt_par(const char *string, vrna_param_t *parameters));
276 
277 
278 #endif
279 
280 #endif
double print_energy
printing threshold for use with logML
vrna_subopt_solution_t * vrna_subopt(vrna_fold_compound_t *vc, int delta, int sorted, FILE *fp)
Returns list of subopt structures or writes to fp.
SOLUTION * zukersubopt_par(const char *string, vrna_param_t *parameters)
Compute Zuker type suboptimal structures.
Solution element from subopt.c.
Definition: subopt.h:51
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.
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:454
int subopt_sorted
Sort output by energy.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:55
Various data structures and pre-processor macros.
vrna_subopt_solution_t * vrna_subopt_zuker(vrna_fold_compound_t *vc)
Compute Zuker type suboptimal structures.
void vrna_subopt_cb(vrna_fold_compound_t *vc, int delta, vrna_subopt_callback *cb, void *data)
Generate suboptimal structures within an energy band arround the MFE.
Functions to deal with sets of energy parameters.
SOLUTION * zukersubopt(const char *string)
Compute Zuker type suboptimal structures.
char * structure
Structure in dot-bracket notation.
Definition: subopt.h:53
#define MAXDOS
Maximum density of states discretization for subopt.
Definition: subopt.h:59
void( vrna_subopt_callback)(const char *stucture, float energy, void *data)
Callback for vrna_subopt_cb()
Definition: subopt.h:32
SOLUTION * subopt(char *seq, char *structure, int delta, FILE *fp)
Returns list of subopt structures or writes to fp.
float energy
Free Energy of structure in kcal/mol.
Definition: subopt.h:52
SOLUTION * subopt_circ(char *seq, char *sequence, int delta, FILE *fp)
Returns list of circular subopt structures or writes to fp.
int density_of_states[MAXDOS+1]
The Density of States.