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cofold.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_COFOLD_H
2 #define VIENNA_RNA_PACKAGE_COFOLD_H
3
4 #include <ViennaRNA/data_structures.h>
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 *sequence,
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
update_cofold_params
void update_cofold_params(void)
Recalculate parameters.
cofold_par
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.
vrna_param_s
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
export_cofold_arrays
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.
update_cofold_params_par
void update_cofold_params_par(vrna_param_t *parameters)
Recalculate parameters.
export_cofold_arrays_gq
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)
data_structures.h
get_monomere_mfes
void get_monomere_mfes(float *e1, float *e2)
get_monomer_free_energies
free_co_arrays
void free_co_arrays(void)
Free memory occupied by cofold()
params.h
vrna_cofold
float vrna_cofold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequ...
cofold
float cofold(const char *sequence, char *structure)
Compute the minimum free energy of two interacting RNA molecules.
mfe.h
MFE calculations for single RNA sequences.
initialize_cofold
void initialize_cofold(int length)