RNAlib-2.2.7
Suboptimal structures within an energy band arround the MFE
+ Collaboration diagram for Suboptimal structures within an energy band arround the MFE:

Functions

vrna_subopt_solution_tvrna_subopt (vrna_fold_compound_t *vc, int delta, int sorted, FILE *fp)
 Returns list of subopt structures or writes to fp. More...
 
SOLUTIONsubopt (char *seq, char *structure, int delta, FILE *fp)
 Returns list of subopt structures or writes to fp. More...
 
SOLUTIONsubopt_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.
 
SOLUTIONsubopt_circ (char *seq, char *sequence, int delta, FILE *fp)
 Returns list of circular subopt structures or writes to fp. More...
 

Variables

double print_energy
 printing threshold for use with logML
 
int subopt_sorted
 Sort output by energy.
 

Detailed Description

Function Documentation

vrna_subopt_solution_t* vrna_subopt ( vrna_fold_compound_t vc,
int  delta,
int  sorted,
FILE *  fp 
)

#include <ViennaRNA/subopt.h>

Returns list of subopt structures or writes to fp.

This function produces all suboptimal secondary structures within 'delta' * 0.01 kcal/mol of the optimum, see [17]. The results are either directly written to a 'fp' (if 'fp' is not NULL), or (fp==NULL) returned in a #vrna_subopt_solution_t * list terminated by an entry were the 'structure' member is NULL.

See also
vrna_subopt_zuker()
Parameters
vc
delta
sortedSort results by energy in ascending order
fp
Returns
SOLUTION* subopt ( char *  seq,
char *  structure,
int  delta,
FILE *  fp 
)

#include <ViennaRNA/subopt.h>

Returns list of subopt structures or writes to fp.

This function produces all suboptimal secondary structures within 'delta' * 0.01 kcal/mol of the optimum. The results are either directly written to a 'fp' (if 'fp' is not NULL), or (fp==NULL) returned in a #SOLUTION * list terminated by an entry were the 'structure' pointer is NULL.

Parameters
seq
structure
delta
fp
Returns
SOLUTION* subopt_circ ( char *  seq,
char *  sequence,
int  delta,
FILE *  fp 
)

#include <ViennaRNA/subopt.h>

Returns list of circular subopt structures or writes to fp.

This function is similar to subopt() but calculates secondary structures assuming the RNA sequence to be circular instead of linear

Parameters
seq
sequence
delta
fp
Returns