RNAlib-2.5.0
cofold.h
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1 #ifndef VIENNA_RNA_PACKAGE_COFOLD_H
2 #define VIENNA_RNA_PACKAGE_COFOLD_H
3 
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 
26 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
27 
42 DEPRECATED(float
43  cofold(const char *sequence,
44  char *structure),
45  "Use vrna_cofold() instead");
46 
54 DEPRECATED(float
55  cofold_par(const char *string,
56  char *structure,
57  vrna_param_t *parameters,
58  int is_constrained),
59  "Use the new API and vrna_mfe_dimer() instead");
60 
72 DEPRECATED(void
73  free_co_arrays(void),
74  "This function is obsolete");
75 
82 DEPRECATED(void
84  "This function is obsolete");
85 
92 DEPRECATED(void
94  "Use the new API with vrna_fold_compound_t instead");
95 
96 
118 DEPRECATED(void
119  export_cofold_arrays_gq(int **f5_p,
120  int **c_p,
121  int **fML_p,
122  int **fM1_p,
123  int **fc_p,
124  int **ggg_p,
125  int **indx_p,
126  char **ptype_p),
127  "Use the new API with vrna_fold_compound_t instead");
128 
149 DEPRECATED(void
150  export_cofold_arrays(int **f5_p,
151  int **c_p,
152  int **fML_p,
153  int **fM1_p,
154  int **fc_p,
155  int **indx_p,
156  char **ptype_p),
157  "Use the new API with vrna_fold_compound_t instead");
158 
159 
166 DEPRECATED(void
167  initialize_cofold(int length),
168  "This function is obsolete");
169 
170 #endif
171 
172 #endif
Various data structures and pre-processor macros.
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
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.
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)
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.
void update_cofold_params_par(vrna_param_t *parameters)
Recalculate parameters.
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.
void initialize_cofold(int length)
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
Functions to deal with sets of energy parameters.