1#ifndef VIENNA_RNA_PACKAGE_COFOLD_H
2#define VIENNA_RNA_PACKAGE_COFOLD_H
8#ifdef VRNA_WARN_DEPRECATED
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
26#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
43 cofold(
const char *sequence,
45 "Use vrna_cofold() instead");
59 "Use the new API and vrna_mfe_dimer() instead");
74 "This function is obsolete");
84 "This function is obsolete");
94 "Use the new API with vrna_fold_compound_t instead");
127 "Use the new API with vrna_fold_compound_t instead");
157 "Use the new API with vrna_fold_compound_t instead");
168 "This function is obsolete");
Various data structures and pre-processor macros.
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
void update_cofold_params(void)
Recalculate parameters.
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 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)
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.
void update_cofold_params_par(vrna_param_t *parameters)
Recalculate parameters.
void free_co_arrays(void)
Free memory occupied by cofold()
float cofold(const char *sequence, char *structure)
Compute the minimum free energy of two interacting RNA molecules.
void initialize_cofold(int length)
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
Functions to deal with sets of energy parameters.