RNAlib-2.4.14
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 
31 typedef struct vrna_subopt_sol_s vrna_subopt_solution_t;
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 
62 #include <ViennaRNA/datastructures/basic.h>
63 #include <ViennaRNA/fold_compound.h>
64 #include <ViennaRNA/params/basic.h>
65 
66 
70 struct vrna_subopt_sol_s {
71  float energy;
72  char *structure;
73 };
74 
78 #define MAXDOS 1000
79 
117 vrna_subopt_solution_t *
118 vrna_subopt(vrna_fold_compound_t *vc,
119  int delta,
120  int sorted,
121  FILE *fp);
122 
157 void
158 vrna_subopt_cb( vrna_fold_compound_t *vc,
159  int delta,
160  vrna_subopt_callback *cb,
161  void *data);
162 
187 vrna_subopt_solution_t *
188 vrna_subopt_zuker(vrna_fold_compound_t *vc);
189 
196 extern double print_energy;
197 
204 extern int subopt_sorted;
205 
222 extern int density_of_states[MAXDOS+1];
223  /* End of group dos */
225 
226 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
227 
245 DEPRECATED(SOLUTION *subopt (char *seq, char *structure, int delta, FILE *fp),
246 "Use vrna_subopt() or vrna_subopt_cb() instead");
247 
253 DEPRECATED(SOLUTION *subopt_par(char *seq, char *structure, vrna_param_t *parameters, int delta, int is_constrained, int is_circular, FILE *fp),
254 "Use vrna_subopt() or vrna_subopt_cb() instead");
255 
270 DEPRECATED(SOLUTION *subopt_circ(char *seq, char *sequence, int delta, FILE *fp),
271 "Use vrna_subopt() or vrna_subopt_cb() instead");
272 
287 DEPRECATED(SOLUTION *zukersubopt(const char *string),
288 "Use vrna_subopt_zuker() instead");
289 
298 DEPRECATED(SOLUTION *zukersubopt_par(const char *string, vrna_param_t *parameters),
299 "Use vrna_subopt_zuker() instead");
300 
301 
302 #endif
303 
304 #endif
print_energy
double print_energy
printing threshold for use with logML
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.
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:70
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: fold_compound.h:132
subopt_sorted
int subopt_sorted
Sort output by energy.
vrna_param_s
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
basic.h
Various data structures and pre-processor macros.
vrna_subopt_zuker
vrna_subopt_solution_t * vrna_subopt_zuker(vrna_fold_compound_t *vc)
Compute Zuker type suboptimal structures.
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.
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:72
MAXDOS
#define MAXDOS
Maximum density of states discretization for subopt.
Definition: subopt.h:78
vrna_subopt_callback
void( vrna_subopt_callback)(const char *stucture, float energy, void *data)
Callback for vrna_subopt_cb()
Definition: subopt.h:48
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:71
basic.h
Functions to deal with sets of energy parameters.
fold_compound.h
The Basic Fold Compound API.
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.