RNAlib-2.2.0-RC2
cofold.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_COFOLD_H
2 #define VIENNA_RNA_PACKAGE_COFOLD_H
3 
5 #include <ViennaRNA/params.h>
6 
7 #ifdef __GNUC__
8 #define DEPRECATED(func) func __attribute__ ((deprecated))
9 #else
10 #define DEPRECATED(func) func
11 #endif
12 
68 DEPRECATED(float
69 cofold( const char *sequence,
70  char *structure));
71 
78 DEPRECATED(float
79 cofold_par( const char *string,
80  char *structure,
81  vrna_param_t *parameters,
82  int is_constrained));
83 
96  char *structure);
97 
109 char *vrna_cut_point_insert(const char *string,
110  int cp);
111 
124 char *vrna_cut_point_remove(const char *string,
125  int *cp);
126 
136 DEPRECATED(void free_co_arrays(void));
137 
141 DEPRECATED(void update_cofold_params(void));
142 
146 DEPRECATED(void update_cofold_params_par(vrna_param_t *parameters));
147 
148 
169 DEPRECATED(void export_cofold_arrays_gq(int **f5_p,
170  int **c_p,
171  int **fML_p,
172  int **fM1_p,
173  int **fc_p,
174  int **ggg_p,
175  int **indx_p,
176  char **ptype_p));
177 
197 DEPRECATED(void export_cofold_arrays( int **f5_p,
198  int **c_p,
199  int **fML_p,
200  int **fM1_p,
201  int **fc_p,
202  int **indx_p,
203  char **ptype_p));
204 
205 
224 DEPRECATED(SOLUTION *zukersubopt(const char *string));
225 
234 DEPRECATED(SOLUTION *zukersubopt_par(const char *string, vrna_param_t *parameters));
235 
249 
258 DEPRECATED(void get_monomere_mfes( float *e1, float *e2));
259 
260 
265 DEPRECATED(void initialize_cofold(int length));
266 
267 #endif
char * vrna_cut_point_insert(const char *string, int cp)
Add a separating '&' character into a string according to cut-point position.
SOLUTION * zukersubopt_par(const char *string, vrna_param_t *parameters)
Compute Zuker type suboptimal structures.
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.
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 get_monomere_mfes(float *e1, float *e2)
get_monomer_free_energies
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)
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:689
Solution element from subopt.c.
Definition: data_structures.h:114
float vrna_cofold(vrna_fold_compound *vc, char *structure)
Compute the minimum free energy of two interacting RNA molecules.
void free_co_arrays(void)
Free memory occupied by cofold()
SOLUTION * zukersubopt(const char *string)
Compute Zuker type suboptimal structures.
char * vrna_cut_point_remove(const char *string, int *cp)
Remove a separating '&' character from a string.
float cofold(const char *sequence, char *structure)
Compute the minimum free energy of two interacting RNA molecules.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:41
SOLUTION * vrna_zukersubopt(vrna_fold_compound *vc)
Compute Zuker type suboptimal structures.
void initialize_cofold(int length)