cofold.h File Reference

MFE version of cofolding routines. More...

Include dependency graph for cofold.h:

Go to the source code of this file.

Functions
float	cofold (const char *sequence, char *structure)
	Compute the minimum free energy of two interacting RNA molecules. More...
float	cofold_par (const char *string, char *structure, paramT *parameters, int is_constrained)
	Compute the minimum free energy of two interacting RNA molecules.
void	free_co_arrays (void)
	Free memory occupied by cofold()
void	update_cofold_params (void)
	Recalculate parameters.
void	export_cofold_arrays_gq (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **ggg_p, int **indx_p, char **ptype_p)
	Export the arrays of partition function cofold (with gquadruplex support) More...
void	export_cofold_arrays (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **indx_p, char **ptype_p)
	Export the arrays of partition function cofold. More...
SOLUTION *	zukersubopt (const char *string)
	Compute Zuker type suboptimal structures. More...
SOLUTION *	zukersubopt_par (const char *string, paramT *parameters)
	Compute Zuker type suboptimal structures.
void	get_monomere_mfes (float *e1, float *e2)
	get_monomer_free_energies More...
void	initialize_cofold (int length)

Detailed Description

MFE version of cofolding routines.

This file includes (almost) all function declarations within the RNAlib that are related to MFE Cofolding... This also includes the Zuker suboptimals calculations, since they are implemented using the cofold routines.

Function Documentation

void get_monomere_mfes	(	float *	e1,
		float *	e2
	)

get_monomer_free_energies

Export monomer free energies out of cofold arrays

Parameters

e1	A pointer to a variable where the energy of molecule A will be written to
e2	A pointer to a variable where the energy of molecule B will be written to

void initialize_cofold

(

int

length

)

allocate arrays for folding

Deprecated:

{This function is obsolete and will be removed soon!}