RNAlib-2.5.1
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
42DEPRECATED(float
43 cofold(const char *sequence,
44 char *structure),
45 "Use vrna_cofold() instead");
46
54DEPRECATED(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
72DEPRECATED(void
73 free_co_arrays(void),
74 "This function is obsolete");
75
82DEPRECATED(void
84 "This function is obsolete");
85
92DEPRECATED(void
94 "Use the new API with vrna_fold_compound_t instead");
95
96
118DEPRECATED(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
149DEPRECATED(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
166DEPRECATED(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168 "This function is obsolete");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.