findpath.h File Reference

Compute direct refolding paths between two secondary structures. More...

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Functions
int	find_saddle (const char *seq, const char *struc1, const char *struc2, int max)
	Find energy of a saddle point between 2 structures (serch only direct path) More...
path_t *	get_path (const char *seq, const char *s1, const char *s2, int maxkeep)
	Find refolding path between 2 structures (serch only direct path) More...
void	free_path (path_t *path)
	Free memory allocated by get_path() function. More...

Detailed Description

Compute direct refolding paths between two secondary structures.

Function Documentation

int find_saddle	(	const char *	seq,
		const char *	struc1,
		const char *	struc2,
		int	max
	)

Find energy of a saddle point between 2 structures (serch only direct path)

Parameters

seq	RNA sequence
struc1	A pointer to the character array where the first secondary structure in dot-bracket notation will be written to
struc2	A pointer to the character array where the second secondary structure in dot-bracket notation will be written to
max	integer how many strutures are being kept during the search

Returns

the saddle energy in 10cal/mol

path_t* get_path	(	const char *	seq,
		const char *	s1,
		const char *	s2,
		int	maxkeep
	)

Find refolding path between 2 structures (serch only direct path)

Parameters

seq	RNA sequence
s1	A pointer to the character array where the first secondary structure in dot-bracket notation will be written to
s2	A pointer to the character array where the second secondary structure in dot-bracket notation will be written to
maxkeep	integer how many strutures are being kept during the search

Returns

direct refolding path between two structures

void free_path

(

path_t *

path

)

Free memory allocated by get_path() function.

Parameters

path	pointer to memory to be freed