RNAlib-2.2.0RC0
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 
6 #ifdef __GNUC__
7 #define DEPRECATED(func) func __attribute__ ((deprecated))
8 #else
9 #define DEPRECATED(func) func
10 #endif
11 
67 DEPRECATED(float
68 cofold( const char *sequence,
69  char *structure));
70 
77 DEPRECATED(float
78 cofold_par( const char *string,
79  char *structure,
80  paramT *parameters,
81  int is_constrained));
82 
95  char *structure);
96 
108 char *vrna_cut_point_insert(const char *string,
109  int cp);
110 
123 char *vrna_cut_point_remove(const char *string,
124  int *cp);
125 
135 DEPRECATED(void free_co_arrays(void));
136 
140 DEPRECATED(void update_cofold_params(void));
141 
145 DEPRECATED(void update_cofold_params_par(paramT *parameters));
146 
147 
168 DEPRECATED(void export_cofold_arrays_gq(int **f5_p,
169  int **c_p,
170  int **fML_p,
171  int **fM1_p,
172  int **fc_p,
173  int **ggg_p,
174  int **indx_p,
175  char **ptype_p));
176 
196 DEPRECATED(void export_cofold_arrays( int **f5_p,
197  int **c_p,
198  int **fML_p,
199  int **fM1_p,
200  int **fc_p,
201  int **indx_p,
202  char **ptype_p));
203 
204 
223 DEPRECATED(SOLUTION *zukersubopt(const char *string));
224 
233 DEPRECATED(SOLUTION *zukersubopt_par(const char *string, paramT *parameters));
234 
248 
257 DEPRECATED(void get_monomere_mfes( float *e1, float *e2));
258 
259 
264 DEPRECATED(void initialize_cofold(int length));
265 
266 #endif
char * vrna_cut_point_insert(const char *string, int cp)
Add a separating '&' character into a string according to cut-point position.
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.
The datastructure that contains temperature scaled energy parameters.
Definition: data_structures.h:180
void update_cofold_params_par(paramT *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)
Definition: data_structures.h:359
Solution element from subopt.c.
Definition: data_structures.h:442
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
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()
float cofold_par(const char *string, char *structure, paramT *parameters, int is_constrained)
Compute the minimum free energy of two interacting RNA molecules.
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.
SOLUTION * vrna_zukersubopt(vrna_fold_compound *vc)
Compute Zuker type suboptimal structures.
SOLUTION * zukersubopt_par(const char *string, paramT *parameters)
Compute Zuker type suboptimal structures.
void initialize_cofold(int length)