cofold.h
Go to the documentation of this file.
#ifndef VIENNA_RNA_PACKAGE_COFOLD_H
#define VIENNA_RNA_PACKAGE_COFOLD_H
#include <ViennaRNA/data_structures.h>
#include <ViennaRNA/params.h>
#include <ViennaRNA/mfe.h>
#ifdef DEPRECATION_WARNINGS
# ifdef __GNUC__
# define DEPRECATED(func) func __attribute__ ((deprecated))
# else
# define DEPRECATED(func) func
# endif
#else
# define DEPRECATED(func) func
#endif
/* make this interface backward compatible with RNAlib < 2.2.0 */
#define VRNA_BACKWARD_COMPAT
float
vrna_cofold(const char *string,
char *structure);
#ifdef VRNA_BACKWARD_COMPAT
DEPRECATED(float
cofold( const char *sequence,
char *structure));
DEPRECATED(float
cofold_par( const char *string,
char *structure,
vrna_param_t *parameters,
int is_constrained));
DEPRECATED(void free_co_arrays(void));
DEPRECATED(void update_cofold_params(void));
DEPRECATED(void update_cofold_params_par(vrna_param_t *parameters));
DEPRECATED(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));
DEPRECATED(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));
DEPRECATED(void get_monomere_mfes( float *e1, float *e2));
DEPRECATED(void initialize_cofold(int length));
#endif
#endif
update_cofold_params
void update_cofold_params(void)
Recalculate parameters.
cofold_par
float cofold_par(const char *string, char *structure, vrna_param_t *parameters, int is_constrained)
Compute the minimum free energy of two interacting RNA molecules.
vrna_param_s
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
export_cofold_arrays
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.
update_cofold_params_par
void update_cofold_params_par(vrna_param_t *parameters)
Recalculate parameters.
export_cofold_arrays_gq
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)
data_structures.h
get_monomere_mfes
void get_monomere_mfes(float *e1, float *e2)
get_monomer_free_energies
free_co_arrays
void free_co_arrays(void)
Free memory occupied by cofold()
params.h
cofold
float cofold(const char *sequence, char *structure)
Compute the minimum free energy of two interacting RNA molecules.
vrna_cofold
float vrna_cofold(const char *string, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequ...
mfe.h
MFE calculations for single RNA sequences.
initialize_cofold
void initialize_cofold(int length)