2 #ifndef VIENNA_RNA_PACKAGE_SUBOPT_H 3 #define VIENNA_RNA_PACKAGE_SUBOPT_H 5 #ifdef DEPRECATION_WARNINGS 7 # define DEPRECATED(func) func __attribute__ ((deprecated)) 9 # define DEPRECATED(func) func 12 # define DEPRECATED(func) func 24 #define VRNA_BACKWARD_COMPAT 37 #ifdef VRNA_BACKWARD_COMPAT 210 #ifdef VRNA_BACKWARD_COMPAT 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:54
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:424
int subopt_sorted
Sort output by energy.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
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.
SOLUTION * zukersubopt(const char *string)
Compute Zuker type suboptimal structures.
char * structure
Structure in dot-bracket notation.
Definition: subopt.h:56
#define MAXDOS
Maximum density of states discretization for subopt.
Definition: subopt.h:62
void( vrna_subopt_callback)(const char *stucture, float energy, void *data)
Callback for vrna_subopt_cb()
Definition: subopt.h:35
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:55
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.