RNAlib-2.2.7

MFE version of cofolding routines. More...

+ Include dependency graph for cofold.h:

Go to the source code of this file.

Functions

float vrna_cofold (const char *string, char *structure)
 Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequences. More...
 
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, vrna_param_t *parameters, int is_constrained)
 Compute the minimum free energy of two interacting RNA molecules. More...
 
void free_co_arrays (void)
 Free memory occupied by cofold() More...
 
void update_cofold_params (void)
 Recalculate parameters. More...
 
void update_cofold_params_par (vrna_param_t *parameters)
 Recalculate parameters. More...
 
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...
 
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.