RNAlib-2.3.1
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 
59 float
60 vrna_cofold(const char *sequence,
61  char *structure);
62 
63 #ifdef VRNA_BACKWARD_COMPAT
64 
79 DEPRECATED(float
80 cofold( const char *sequence,
81  char *structure));
82 
89 DEPRECATED(float
90 cofold_par( const char *string,
91  char *structure,
92  vrna_param_t *parameters,
93  int is_constrained));
94 
104 DEPRECATED(void free_co_arrays(void));
105 
110 DEPRECATED(void update_cofold_params(void));
111 
116 DEPRECATED(void update_cofold_params_par(vrna_param_t *parameters));
117 
118 
139 DEPRECATED(void export_cofold_arrays_gq(int **f5_p,
140  int **c_p,
141  int **fML_p,
142  int **fM1_p,
143  int **fc_p,
144  int **ggg_p,
145  int **indx_p,
146  char **ptype_p));
147 
167 DEPRECATED(void export_cofold_arrays( int **f5_p,
168  int **c_p,
169  int **fML_p,
170  int **fM1_p,
171  int **fc_p,
172  int **indx_p,
173  char **ptype_p));
174 
175 
176 
186 DEPRECATED(void get_monomere_mfes( float *e1, float *e2));
187 
188 
193 DEPRECATED(void initialize_cofold(int length));
194 
195 #endif
196 
202 #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:55
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)
Various data structures and pre-processor macros.
void get_monomere_mfes(float *e1, float *e2)
get_monomer_free_energies
void free_co_arrays(void)
Free memory occupied by cofold()
Functions to deal with sets of energy parameters.
float vrna_cofold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequ...
float cofold(const char *sequence, char *structure)
Compute the minimum free energy of two interacting RNA molecules.
MFE calculations for single RNA sequences.
void initialize_cofold(int length)