subopt.h
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/* subopt.h */
#ifndef VIENNA_RNA_PACKAGE_SUBOPT_H
#define VIENNA_RNA_PACKAGE_SUBOPT_H
#ifdef DEPRECATION_WARNINGS
# ifdef __GNUC__
# define DEPRECATED(func) func __attribute__ ((deprecated))
# else
# define DEPRECATED(func) func
# endif
#else
# define DEPRECATED(func) func
#endif
#define VRNA_BACKWARD_COMPAT
typedef struct vrna_subopt_sol_s vrna_subopt_solution_t;
#ifdef VRNA_BACKWARD_COMPAT
typedef struct vrna_subopt_sol_s SOLUTION;
#endif
#include <ViennaRNA/data_structures.h>
#include <ViennaRNA/params.h>
struct vrna_subopt_sol_s {
float energy;
char *structure;
};
#define MAXDOS 1000
vrna_subopt_solution_t *
vrna_subopt(vrna_fold_compound_t *vc,
int delta,
int sorted,
FILE *fp);
vrna_subopt_solution_t *
vrna_subopt_zuker(vrna_fold_compound_t *vc);
extern double print_energy;
extern int subopt_sorted;
extern int density_of_states[MAXDOS+1];
/* End of group dos */
#ifdef VRNA_BACKWARD_COMPAT
DEPRECATED(SOLUTION *subopt (char *seq, char *structure, int delta, FILE *fp));
DEPRECATED(SOLUTION *subopt_par(char *seq, char *structure, vrna_param_t *parameters, int delta, int is_constrained, int is_circular, FILE *fp));
DEPRECATED(SOLUTION *subopt_circ(char *seq, char *sequence, int delta, FILE *fp));
DEPRECATED(SOLUTION *zukersubopt(const char *string));
DEPRECATED(SOLUTION *zukersubopt_par(const char *string, vrna_param_t *parameters));
#endif
#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:48
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:390
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
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:50
MAXDOS
#define MAXDOS
Maximum density of states discretization for subopt.
Definition: subopt.h:56
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:49
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.