RNAlib-2.4.16
subopt.h
Go to the documentation of this file.
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 
60 #include <stdio.h>
61 
64 #include <ViennaRNA/params/basic.h>
65 
66 
71  float energy;
72  char *structure;
73 };
74 
78 #define MAXDOS 1000
79 
87 #define VRNA_UNSORTED 0
88 #define VRNA_SORT_BY_ENERGY_LEXICOGRAPHIC_ASC 1
89 #define VRNA_SORT_BY_ENERGY_ASC 2
90 
123  int delta,
124  int sorted,
125  FILE *fp);
126 
161 void
163  int delta,
165  void *data);
166 
193 
200 extern double print_energy;
201 
208 extern int subopt_sorted;
209 
226 extern int density_of_states[MAXDOS+1];
227  /* End of group dos */
229 
230 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
231 
249 DEPRECATED(SOLUTION *subopt (char *seq, char *structure, int delta, FILE *fp),
250 "Use vrna_subopt() or vrna_subopt_cb() instead");
251 
257 DEPRECATED(SOLUTION *subopt_par(char *seq, char *structure, vrna_param_t *parameters, int delta, int is_constrained, int is_circular, FILE *fp),
258 "Use vrna_subopt() or vrna_subopt_cb() instead");
259 
274 DEPRECATED(SOLUTION *subopt_circ(char *seq, char *sequence, int delta, FILE *fp),
275 "Use vrna_subopt() or vrna_subopt_cb() instead");
276 
291 DEPRECATED(SOLUTION *zukersubopt(const char *string),
292 "Use vrna_subopt_zuker() instead");
293 
302 DEPRECATED(SOLUTION *zukersubopt_par(const char *string, vrna_param_t *parameters),
303 "Use vrna_subopt_zuker() instead");
304 
305 
306 #endif
307 
308 #endif
vrna_subopt
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.
print_energy
double print_energy
printing threshold for use with logML
vrna_param_s
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
subopt_sorted
int subopt_sorted
Sort output by energy.
subopt_par
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.
density_of_states
int density_of_states[MAXDOS+1]
The Density of States.
vrna_subopt_cb
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.
basic.h
Various data structures and pre-processor macros.
vrna_subopt_sol_s::energy
float energy
Free Energy of structure in kcal/mol.
Definition: subopt.h:71
subopt
SOLUTION * subopt(char *seq, char *structure, int delta, FILE *fp)
Returns list of subopt structures or writes to fp.
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
MAXDOS
#define MAXDOS
Maximum density of states discretization for subopt.
Definition: subopt.h:78
zukersubopt_par
SOLUTION * zukersubopt_par(const char *string, vrna_param_t *parameters)
Compute Zuker type suboptimal structures.
zukersubopt
SOLUTION * zukersubopt(const char *string)
Compute Zuker type suboptimal structures.
vrna_subopt_callback
void() vrna_subopt_callback(const char *stucture, float energy, void *data)
Callback for vrna_subopt_cb()
Definition: subopt.h:48
vrna_subopt_sol_s::structure
char * structure
Structure in dot-bracket notation.
Definition: subopt.h:72
fold_compound.h
The Basic Fold Compound API.
vrna_subopt_zuker
vrna_subopt_solution_t * vrna_subopt_zuker(vrna_fold_compound_t *vc)
Compute Zuker type suboptimal structures.
subopt_circ
SOLUTION * subopt_circ(char *seq, char *sequence, int delta, FILE *fp)
Returns list of circular subopt structures or writes to fp.
basic.h
Functions to deal with sets of energy parameters.
vrna_subopt_sol_s
Solution element from subopt.c.
Definition: subopt.h:70