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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 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
29 typedef struct vrna_subopt_sol_s vrna_subopt_solution_t;
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
47 #include <ViennaRNA/data_structures.h>
48 #include <ViennaRNA/params.h>
49
50
54 struct vrna_subopt_sol_s {
55 float energy;
56 char *structure;
57 };
58
62 #define MAXDOS 1000
63
89 vrna_subopt_solution_t *
90 vrna_subopt(vrna_fold_compound_t *vc,
91 int delta,
92 int sorted,
93 FILE *fp);
94
117 void
118 vrna_subopt_cb( vrna_fold_compound_t *vc,
119 int delta,
120 vrna_subopt_callback *cb,
121 void *data);
122
147 vrna_subopt_solution_t *
148 vrna_subopt_zuker(vrna_fold_compound_t *vc);
149
156 extern double print_energy;
157
164 extern int subopt_sorted;
165
182 extern int density_of_states[MAXDOS+1];
183 /* End of group dos */
185
186 #ifdef VRNA_BACKWARD_COMPAT
187
205 DEPRECATED(SOLUTION *subopt (char *seq, char *structure, int delta, FILE *fp));
206
212 DEPRECATED(SOLUTION *subopt_par(char *seq, char *structure, vrna_param_t *parameters, int delta, int is_constrained, int is_circular, FILE *fp));
213
228 DEPRECATED(SOLUTION *subopt_circ(char *seq, char *sequence, int delta, FILE *fp));
229
244 DEPRECATED(SOLUTION *zukersubopt(const char *string));
245
254 DEPRECATED(SOLUTION *zukersubopt_par(const char *string, vrna_param_t *parameters));
255
256
257 #endif
258
259 #endif
print_energy
double print_energy
printing threshold for use with logML
zukersubopt_par
SOLUTION * zukersubopt_par(const char *string, vrna_param_t *parameters)
Compute Zuker type suboptimal structures.
vrna_subopt_sol_s
Solution element from subopt.c.
Definition: subopt.h:54
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.
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:424
subopt_sorted
int subopt_sorted
Sort output by energy.
vrna_param_s
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
data_structures.h
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.
params.h
zukersubopt
SOLUTION * zukersubopt(const char *string)
Compute Zuker type suboptimal structures.
vrna_subopt_sol_s::structure
char * structure
Structure in dot-bracket notation.
Definition: subopt.h:56
MAXDOS
#define MAXDOS
Maximum density of states discretization for subopt.
Definition: subopt.h:62
vrna_subopt_callback
void( vrna_subopt_callback)(const char *stucture, float energy, void *data)
Callback for vrna_subopt_cb()
Definition: subopt.h:35
subopt
SOLUTION * subopt(char *seq, char *structure, int delta, FILE *fp)
Returns list of subopt structures or writes to fp.
vrna_subopt_sol_s::energy
float energy
Free Energy of structure in kcal/mol.
Definition: subopt.h:55
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.
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.
density_of_states
int density_of_states[MAXDOS+1]
The Density of States.