RNAsubopt and density of states declarations. More...

Include dependency graph for subopt.h:

Data Structures
struct	vrna_subopt_sol_s
	Solution element from subopt.c. More...

Macros
#define	MAXDOS 1000
	Maximum density of states discretization for subopt.

Typedefs
typedef struct vrna_subopt_sol_s	vrna_subopt_solution_t
	Typename for the subopt solution list repesenting data structure vrna_subopt_sol_s.

typedef void(	vrna_subopt_callback) (const char stucture, float energy, void data)
	Callback for vrna_subopt_cb() More...

typedef struct vrna_subopt_sol_s	SOLUTION
	Backward compatibility typedef for vrna_subopt_sol_s. More...

Functions
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. More...

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. More...

vrna_subopt_solution_t *	vrna_subopt_zuker (vrna_fold_compound_t *vc)
	Compute Zuker type suboptimal structures. More...

SOLUTION *	subopt (char seq, char structure, int delta, FILE *fp)
	Returns list of subopt structures or writes to fp. More...

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 *	subopt_circ (char seq, char sequence, int delta, FILE *fp)
	Returns list of circular subopt structures or writes to fp. More...

SOLUTION *	zukersubopt (const char *string)
	Compute Zuker type suboptimal structures. More...

SOLUTION *	zukersubopt_par (const char string, vrna_param_t parameters)
	Compute Zuker type suboptimal structures. More...

Variables
double	print_energy
	printing threshold for use with logML

int	subopt_sorted
	Sort output by energy.

int	density_of_states [MAXDOS+1]
	The Density of States. More...

Detailed Description

RNAsubopt and density of states declarations.

Typedef Documentation

Backward compatibility typedef for vrna_subopt_sol_s.