RNAlib-2.4.5
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 VRNA_WARN_DEPRECATED
9 # if defined(__clang__)
10 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
11 # elif defined(__GNUC__)
12 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
13 # else
14 # define DEPRECATED(func, msg) func
15 # endif
16 #else
17 # define DEPRECATED(func, msg) func
18 #endif
19 
58 float
59 vrna_cofold(const char *sequence,
60  char *structure);
61 
62 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
63 
78 DEPRECATED(float
79 cofold( const char *sequence,
80  char *structure),
81  "Use vrna_cofold() instead");
82 
89 DEPRECATED(float
90 cofold_par( const char *string,
91  char *structure,
92  vrna_param_t *parameters,
93  int is_constrained),
94  "Use the new API and vrna_mfe_dimer() instead");
95 
105 DEPRECATED(void free_co_arrays(void),
106  "This function is obsolete");
107 
112 DEPRECATED(void update_cofold_params(void),
113  "This function is obsolete");
114 
119 DEPRECATED(void update_cofold_params_par(vrna_param_t *parameters),
120  "Use the new API with vrna_fold_compound_t instead");
121 
122 
143 DEPRECATED(void export_cofold_arrays_gq(int **f5_p,
144  int **c_p,
145  int **fML_p,
146  int **fM1_p,
147  int **fc_p,
148  int **ggg_p,
149  int **indx_p,
150  char **ptype_p),
151  "Use the new API with vrna_fold_compound_t instead");
152 
172 DEPRECATED(void export_cofold_arrays( int **f5_p,
173  int **c_p,
174  int **fML_p,
175  int **fM1_p,
176  int **fc_p,
177  int **indx_p,
178  char **ptype_p),
179  "Use the new API with vrna_fold_compound_t instead");
180 
181 
182 
192 DEPRECATED(void get_monomere_mfes( float *e1, float *e2),
193  "This function is obsolete");
194 
195 
200 DEPRECATED(void initialize_cofold(int length),
201  "This function is obsolete");
202 
203 #endif
204 
210 #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:56
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.
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
void initialize_cofold(int length)