Suboptimal structures within an energy band arround the MFE

Collaboration diagram for Suboptimal structures within an energy band arround the MFE:

Functions
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, paramT *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...

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

Detailed Description

Function Documentation

SOLUTION* subopt	(	char *	seq,
		char *	structure,
		int	delta,
		FILE *	fp
	)

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
	)

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