H/cofold.h File Reference

MFE version of cofolding routines. More...

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Functions
float	cofold (const char *sequence, char *structure)
	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.
SOLUTION *	zukersubopt (const char *string)
	Compute Zuker type suboptimal structures.
void	get_monomere_mfes (float *e1, float *e2)
	get_monomer_free_energies
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.
void	initialize_cofold (int length)
	allocate arrays for folding

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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.

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Function Documentation

float cofold	(	const char *	sequence,
		char *	structure
	)

Compute the minimum free energy of two interacting RNA molecules.

The code is analog to the fold() function. If cut_point ==-1 results should be the same as with fold().

Parameters:

	sequence	The two sequences concatenated
	structure	Will hold the barcket dot structure of the dimer molecule

Returns:

minimum free energy of the structure

SOLUTION* zukersubopt

(

const char *

string

)

Compute Zuker type suboptimal structures.

Compute Suboptimal structures according to M. Zuker, i.e. for every possible base pair the minimum energy structure containing the resp. base pair. Returns a list of these structures and their energies.

Parameters:

string

RNA sequence

Returns:

List of zuker suboptimal structures

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 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.

Export the cofold arrays for use e.g. in the concentration Computations or suboptimal secondary structure backtracking

Parameters:

	f5_p	A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]
	c_p	A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j
	fML_p	A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem
	fM1_p	A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem
	fc_p	A pointer to the 'fc' array, i.e. array ...
	indx_p	A pointer to the indexing array used for accessing the energy matrices
	ptype_p	A pointer to the ptype array containing the base pair types for each possibility (i,j)

void initialize_cofold

(

int

length

)

allocate arrays for folding

Deprecated:

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