1 #ifndef VIENNA_RNA_PACKAGE_COFOLD_H 2 #define VIENNA_RNA_PACKAGE_COFOLD_H 8 #ifdef VRNA_WARN_DEPRECATED 9 # if defined(__clang__) 10 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg))) 11 # elif defined(__GNUC__) 12 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg))) 14 # define DEPRECATED(func, msg) func 17 # define DEPRECATED(func, msg) func 62 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 79 cofold(
const char *sequence,
81 "Use vrna_cofold() instead");
94 "Use the new API and vrna_mfe_dimer() instead");
106 "This function is obsolete");
113 "This function is obsolete");
120 "Use the new API with vrna_fold_compound_t instead");
151 "Use the new API with vrna_fold_compound_t instead");
179 "Use the new API with vrna_fold_compound_t instead");
193 "This function is obsolete");
201 "This function is obsolete");
void update_cofold_params(void)
Recalculate parameters.
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.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:56
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 update_cofold_params_par(vrna_param_t *parameters)
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)
Various data structures and pre-processor macros.
void get_monomere_mfes(float *e1, float *e2)
get_monomer_free_energies
void free_co_arrays(void)
Free memory occupied by cofold()
Functions to deal with sets of energy parameters.
float vrna_cofold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequ...
float cofold(const char *sequence, char *structure)
Compute the minimum free energy of two interacting RNA molecules.
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
void initialize_cofold(int length)