Revision 65e147fc67310f2f53bbe1c8fc89ab94b02570dc authored by Ronny Lorenz on 04 May 2015, 13:34:04 UTC, committed by Ronny Lorenz on 04 May 2015, 13:34:04 UTC
1 parent 48c40ba
cofold.h
#ifndef __VIENNA_RNA_PACKAGE_COFOLD_H__
#define __VIENNA_RNA_PACKAGE_COFOLD_H__
#include "data_structures.h"
#ifdef __GNUC__
#define DEPRECATED(func) func __attribute__ ((deprecated))
#else
#define DEPRECATED(func) func
#endif
/**
* \file cofold.h
*
* \brief MFE version of cofolding routines
*
* This file includes (almost) all function declarations within the <b>RNAlib</b> that are related to
* MFE Cofolding...
* This also includes the Zuker suboptimals calculations, since they are implemented using the cofold
* routines.
*/
/**
* \brief 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().
*
* \param sequence The two sequences concatenated
* \param structure Will hold the barcket dot structure of the dimer molecule
* \return minimum free energy of the structure
*/
float cofold( const char *sequence,
char *structure);
float cofold_par( const char *string,
char *structure,
paramT *parameters,
int is_constrained);
/**
* \brief Free memory occupied by cofold()
*/
void free_co_arrays(void);
/**
* \brief Recalculate parameters
*/
void update_cofold_params(void);
void update_cofold_params_par(paramT *parameters);
/**
* \brief 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.
*
* \param string RNA sequence
* \return List of zuker suboptimal structures
*/
SOLUTION *zukersubopt(const char *string);
SOLUTION *zukersubopt_par( const char *string,
paramT *parameters);
/**
* \brief get_monomer_free_energies
*
* Export monomer free energies out of cofold arrays
*
* \param e1 A pointer to a variable where the energy of molecule A will be written to
* \param e2 A pointer to a variable where the energy of molecule B will be written to
*/
void get_monomere_mfes( float *e1,
float *e2);
/**
* \brief Export the arrays of partition function cofold
*
* Export the cofold arrays for use e.g. in the concentration
* Computations or suboptimal secondary structure backtracking
*
* \param f5_p A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]
* \param 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
* \param 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
* \param 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
* \param fc_p A pointer to the 'fc' array, i.e. array ...
* \param indx_p A pointer to the indexing array used for accessing the energy matrices
* \param ptype_p A pointer to the ptype array containing the base pair types for each possibility (i,j)
*/
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);
/**
* allocate arrays for folding
* \deprecated{This function is obsolete and will be removed soon!}
*/
DEPRECATED(void initialize_cofold(int length));
#endif
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