RNAlib-2.2.7
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 
27 
28 #ifdef VRNA_BACKWARD_COMPAT
29 
30 typedef struct vrna_subopt_sol_s SOLUTION;
31 
32 #endif
33 
35 #include <ViennaRNA/params.h>
36 
37 
42  float energy;
43  char *structure;
44 };
45 
49 #define MAXDOS 1000
50 
78  int delta,
79  int sorted,
80  FILE *fp);
81 
108 
115 extern double print_energy;
116 
123 extern int subopt_sorted;
124 
141 extern int density_of_states[MAXDOS+1];
142  /* End of group dos */
144 
145 #ifdef VRNA_BACKWARD_COMPAT
146 
164 DEPRECATED(SOLUTION *subopt (char *seq, char *structure, int delta, FILE *fp));
165 
171 DEPRECATED(SOLUTION *subopt_par(char *seq, char *structure, vrna_param_t *parameters, int delta, int is_constrained, int is_circular, FILE *fp));
172 
187 DEPRECATED(SOLUTION *subopt_circ(char *seq, char *sequence, int delta, FILE *fp));
188 
203 DEPRECATED(SOLUTION *zukersubopt(const char *string));
204 
213 DEPRECATED(SOLUTION *zukersubopt_par(const char *string, vrna_param_t *parameters));
214 
215 
216 #endif
217 
218 #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:41
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:390
int subopt_sorted
Sort output by energy.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
SOLUTION * zukersubopt(const char *string)
Compute Zuker type suboptimal structures.
char * structure
Structure in dot-bracket notation.
Definition: subopt.h:43
#define MAXDOS
Maximum density of states discretization for subopt.
Definition: subopt.h:49
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:42
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.