RNAlib-2.2.7
cofold.h
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1 #ifndef VIENNA_RNA_PACKAGE_COFOLD_H
2 #define VIENNA_RNA_PACKAGE_COFOLD_H
3 
5 #include <ViennaRNA/params.h>
6 #include <ViennaRNA/mfe.h>
7 
8 #ifdef DEPRECATION_WARNINGS
9 # ifdef __GNUC__
10 # define DEPRECATED(func) func __attribute__ ((deprecated))
11 # else
12 # define DEPRECATED(func) func
13 # endif
14 #else
15 # define DEPRECATED(func) func
16 #endif
17 
18 /* make this interface backward compatible with RNAlib < 2.2.0 */
19 #define VRNA_BACKWARD_COMPAT
20 
82 float
83 vrna_cofold(const char *string,
84  char *structure);
85 
86 #ifdef VRNA_BACKWARD_COMPAT
87 
102 DEPRECATED(float
103 cofold( const char *sequence,
104  char *structure));
105 
112 DEPRECATED(float
113 cofold_par( const char *string,
114  char *structure,
115  vrna_param_t *parameters,
116  int is_constrained));
117 
127 DEPRECATED(void free_co_arrays(void));
128 
133 DEPRECATED(void update_cofold_params(void));
134 
139 DEPRECATED(void update_cofold_params_par(vrna_param_t *parameters));
140 
141 
162 DEPRECATED(void export_cofold_arrays_gq(int **f5_p,
163  int **c_p,
164  int **fML_p,
165  int **fM1_p,
166  int **fc_p,
167  int **ggg_p,
168  int **indx_p,
169  char **ptype_p));
170 
190 DEPRECATED(void export_cofold_arrays( int **f5_p,
191  int **c_p,
192  int **fML_p,
193  int **fM1_p,
194  int **fc_p,
195  int **indx_p,
196  char **ptype_p));
197 
198 
199 
209 DEPRECATED(void get_monomere_mfes( float *e1, float *e2));
210 
211 
216 DEPRECATED(void initialize_cofold(int length));
217 
218 #endif
219 
225 #endif
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:50
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)
void get_monomere_mfes(float *e1, float *e2)
get_monomer_free_energies
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.
float vrna_cofold(const char *string, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequ...
MFE calculations for single RNA sequences.
void initialize_cofold(int length)