2#ifndef VIENNA_RNA_PACKAGE_SUBOPT_H
3#define VIENNA_RNA_PACKAGE_SUBOPT_H
5#ifdef VRNA_WARN_DEPRECATED
7# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
8# elif defined(__GNUC__)
9# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
11# define DEPRECATED(func, msg) func
14# define DEPRECATED(func, msg) func
52#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
89#define VRNA_UNSORTED 0
90#define VRNA_SORT_BY_ENERGY_LEXICOGRAPHIC_ASC 1
91#define VRNA_SORT_BY_ENERGY_ASC 2
207#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
226DEPRECATED(
SOLUTION *
subopt(
char *seq,
char *structure,
int delta, FILE * fp),
227 "Use vrna_subopt() or vrna_subopt_cb() instead");
237 int is_circular, FILE * fp),
238 "Use vrna_subopt() or vrna_subopt_cb() instead");
255 "Use vrna_subopt() or vrna_subopt_cb() instead");
272 "Use vrna_subopt_zuker() instead");
283 "Use vrna_subopt_zuker() instead");
Various data structures and pre-processor macros.
The Basic Fold Compound API.
int density_of_states[MAXDOS+1]
The Density of States.
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:148
double print_energy
printing threshold for use with logML
SOLUTION * subopt_circ(char *seq, char *sequence, int delta, FILE *fp)
Returns list of circular subopt structures or writes to fp.
int subopt_sorted
Sort output by energy.
SOLUTION * subopt(char *seq, char *structure, int delta, FILE *fp)
Returns list of subopt structures or writes to fp.
void() vrna_subopt_callback(const char *stucture, float energy, void *data)
Callback for vrna_subopt_cb()
Definition: subopt.h:48
void vrna_subopt_cb(vrna_fold_compound_t *fc, int delta, vrna_subopt_callback *cb, void *data)
Generate suboptimal structures within an energy band arround the MFE.
vrna_subopt_solution_t * vrna_subopt(vrna_fold_compound_t *fc, int delta, int sorted, FILE *fp)
Returns list of subopt structures or writes to fp.
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.
SOLUTION * zukersubopt(const char *string)
Compute Zuker type suboptimal structures.
SOLUTION * zukersubopt_par(const char *string, vrna_param_t *parameters)
Compute Zuker type suboptimal structures.
Functions to deal with sets of energy parameters.
Solution element from subopt.c.
Definition: subopt.h:72
char * structure
Structure in dot-bracket notation.
Definition: subopt.h:74
float energy
Free Energy of structure in kcal/mol.
Definition: subopt.h:73
#define MAXDOS
Maximum density of states discretization for subopt.
Definition: subopt.h:80