RNAlib-2.4.14
cofold.h
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1 #ifndef VIENNA_RNA_PACKAGE_COFOLD_H
2 #define VIENNA_RNA_PACKAGE_COFOLD_H
3 
4 #include <ViennaRNA/datastructures/basic.h>
5 #include <ViennaRNA/params/basic.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 
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 free_co_arrays(void),
73  "This function is obsolete");
74 
81 DEPRECATED(void update_cofold_params(void),
82  "This function is obsolete");
83 
90 DEPRECATED(void update_cofold_params_par(vrna_param_t *parameters),
91  "Use the new API with vrna_fold_compound_t instead");
92 
93 
115 DEPRECATED(void export_cofold_arrays_gq(int **f5_p,
116  int **c_p,
117  int **fML_p,
118  int **fM1_p,
119  int **fc_p,
120  int **ggg_p,
121  int **indx_p,
122  char **ptype_p),
123  "Use the new API with vrna_fold_compound_t instead");
124 
145 DEPRECATED(void export_cofold_arrays( int **f5_p,
146  int **c_p,
147  int **fML_p,
148  int **fM1_p,
149  int **fc_p,
150  int **indx_p,
151  char **ptype_p),
152  "Use the new API with vrna_fold_compound_t instead");
153 
154 
155 
166 DEPRECATED(void get_monomere_mfes( float *e1, float *e2),
167  "This function is obsolete");
168 
169 
176 DEPRECATED(void initialize_cofold(int length),
177  "This function is obsolete");
178 
179 #endif
180 
181 #endif
free_co_arrays
void free_co_arrays(void)
Free memory occupied by cofold()
get_monomere_mfes
void get_monomere_mfes(float *e1, float *e2)
get_monomer_free_energies
update_cofold_params_par
void update_cofold_params_par(vrna_param_t *parameters)
Recalculate parameters.
vrna_param_s
The datastructure that contains temperature scaled energy parameters.
Definition: basic.h:57
cofold
float cofold(const char *sequence, char *structure)
Compute the minimum free energy of two interacting RNA molecules.
initialize_cofold
void initialize_cofold(int length)
basic.h
Various data structures and pre-processor macros.
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)
basic.h
Functions to deal with sets of energy 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.
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.
mfe.h
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
update_cofold_params
void update_cofold_params(void)
Recalculate parameters.