RNAlib-2.2.10
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 
24 #define VRNA_BACKWARD_COMPAT
25 
30 
35 typedef void (vrna_subopt_callback)(const char *stucture, float energy, void *data);
36 
37 #ifdef VRNA_BACKWARD_COMPAT
38 
43 typedef struct vrna_subopt_sol_s SOLUTION;
44 
45 #endif
46 
48 #include <ViennaRNA/params.h>
49 
50 
55  float energy;
56  char *structure;
57 };
58 
62 #define MAXDOS 1000
63 
103  int delta,
104  int sorted,
105  FILE *fp);
106 
141 void
143  int delta,
145  void *data);
146 
173 
180 extern double print_energy;
181 
188 extern int subopt_sorted;
189 
206 extern int density_of_states[MAXDOS+1];
207  /* End of group dos */
209 
210 #ifdef VRNA_BACKWARD_COMPAT
211 
229 DEPRECATED(SOLUTION *subopt (char *seq, char *structure, int delta, FILE *fp));
230 
236 DEPRECATED(SOLUTION *subopt_par(char *seq, char *structure, vrna_param_t *parameters, int delta, int is_constrained, int is_circular, FILE *fp));
237 
252 DEPRECATED(SOLUTION *subopt_circ(char *seq, char *sequence, int delta, FILE *fp));
253 
268 DEPRECATED(SOLUTION *zukersubopt(const char *string));
269 
278 DEPRECATED(SOLUTION *zukersubopt_par(const char *string, vrna_param_t *parameters));
279 
280 
281 #endif
282 
283 #endif
double print_energy
printing threshold for use with logML
SOLUTION * zukersubopt_par(const char *string, vrna_param_t *parameters)
Compute Zuker type suboptimal structures.
Solution element from subopt.c.
Definition: subopt.h:54
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:424
int subopt_sorted
Sort output by energy.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
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.
SOLUTION * zukersubopt(const char *string)
Compute Zuker type suboptimal structures.
char * structure
Structure in dot-bracket notation.
Definition: subopt.h:56
#define MAXDOS
Maximum density of states discretization for subopt.
Definition: subopt.h:62
void( vrna_subopt_callback)(const char *stucture, float energy, void *data)
Callback for vrna_subopt_cb()
Definition: subopt.h:35
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:55
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.
vrna_subopt_solution_t * vrna_subopt_zuker(vrna_fold_compound_t *vc)
Compute Zuker type suboptimal structures.
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.