RNAlib-2.4.0
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 # 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 
43 typedef void (vrna_subopt_callback)(const char *stucture, float energy, void *data);
44 
45 #ifdef VRNA_BACKWARD_COMPAT
46 
51 typedef struct vrna_subopt_sol_s SOLUTION;
52 
53 #endif
54 
56 #include <ViennaRNA/params.h>
57 
58 
63  float energy;
64  char *structure;
65 };
66 
70 #define MAXDOS 1000
71 
111  int delta,
112  int sorted,
113  FILE *fp);
114 
149 void
151  int delta,
153  void *data);
154 
181 
188 extern double print_energy;
189 
196 extern int subopt_sorted;
197 
214 extern int density_of_states[MAXDOS+1];
215  /* End of group dos */
217 
218 #ifdef VRNA_BACKWARD_COMPAT
219 
237 DEPRECATED(SOLUTION *subopt (char *seq, char *structure, int delta, FILE *fp));
238 
244 DEPRECATED(SOLUTION *subopt_par(char *seq, char *structure, vrna_param_t *parameters, int delta, int is_constrained, int is_circular, FILE *fp));
245 
260 DEPRECATED(SOLUTION *subopt_circ(char *seq, char *sequence, int delta, FILE *fp));
261 
276 DEPRECATED(SOLUTION *zukersubopt(const char *string));
277 
286 DEPRECATED(SOLUTION *zukersubopt_par(const char *string, vrna_param_t *parameters));
287 
288 
289 #endif
290 
291 #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:62
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:463
int subopt_sorted
Sort output by energy.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:57
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:64
#define MAXDOS
Maximum density of states discretization for subopt.
Definition: subopt.h:70
void( vrna_subopt_callback)(const char *stucture, float energy, void *data)
Callback for vrna_subopt_cb()
Definition: subopt.h:43
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:63
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.