RNAlib-2.4.4
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 
48 typedef void (vrna_subopt_callback)(const char *stucture, float energy, void *data);
49 
50 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
51 
56 typedef struct vrna_subopt_sol_s SOLUTION;
57 
58 #endif
59 
61 #include <ViennaRNA/params.h>
62 
63 
68  float energy;
69  char *structure;
70 };
71 
75 #define MAXDOS 1000
76 
116  int delta,
117  int sorted,
118  FILE *fp);
119 
154 void
156  int delta,
158  void *data);
159 
186 
193 extern double print_energy;
194 
201 extern int subopt_sorted;
202 
219 extern int density_of_states[MAXDOS+1];
220  /* End of group dos */
222 
223 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
224 
242 DEPRECATED(SOLUTION *subopt (char *seq, char *structure, int delta, FILE *fp),
243 "Use vrna_subopt() or vrna_subopt_cb() instead");
244 
250 DEPRECATED(SOLUTION *subopt_par(char *seq, char *structure, vrna_param_t *parameters, int delta, int is_constrained, int is_circular, FILE *fp),
251 "Use vrna_subopt() or vrna_subopt_cb() instead");
252 
267 DEPRECATED(SOLUTION *subopt_circ(char *seq, char *sequence, int delta, FILE *fp),
268 "Use vrna_subopt() or vrna_subopt_cb() instead");
269 
284 DEPRECATED(SOLUTION *zukersubopt(const char *string),
285 "Use vrna_subopt_zuker() instead");
286 
295 DEPRECATED(SOLUTION *zukersubopt_par(const char *string, vrna_param_t *parameters),
296 "Use vrna_subopt_zuker() instead");
297 
298 
299 #endif
300 
301 #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:67
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: fold_compound.h:131
int subopt_sorted
Sort output by energy.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:56
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:69
#define MAXDOS
Maximum density of states discretization for subopt.
Definition: subopt.h:75
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:68
void() vrna_subopt_callback(const char *stucture, float energy, void *data)
Callback for vrna_subopt_cb()
Definition: subopt.h:48
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.